We're seeing the same issue recently. Using PayPay Website Payments Pro module. We've seen up to 6 duplicate orders with 6 charges to the customer's PayPal account. We saw the problem on v1.3x and again after we upgraded to v.1.5.5e (latest).
Below is from the SSL logs (IP address removed). This resulted in two (2) orders and two (2) PayPal charges. I removed all the tokens, userIds, and IP addresses. Should be clean.
[17/May/2017:09:37:19 -0700] "POST /index.php?main_page=checkout_shipping HTTP/1.1" 302 - "https://www.lscoguard.com/index.php?main_page=checkout_shipping" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:37:19 -0700] "GET /index.php?main_page=checkout_payment HTTP/1.1" 200 7535 "https://www.lscoguard.com/index.php?main_page=checkout_shipping" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:37:32 -0700] "POST /index.php?main_page=checkout_confirmation HTTP/1.1" 200 5867 "https://www.lscoguard.com/index.php?main_page=checkout_payment" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:37:33 -0700] "GET /includes/templates/pure_orange_free/buttons/english/button_confirm_order.gif HTTP/1.1" 200 978 "https://www.lscoguard.com/index.php?main_page=checkout_confirmation" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:37:45 -0700] "POST /ipn_main_handler.php?type=ec&markflow=1&clearSess=1&stage=final HTTP/1.1" 302 - "https://www.lscoguard.com/index.php?main_page=checkout_confirmation" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:37:50 -0700] "GET /images/header_pp.jpg HTTP/1.1" 200 3645 "https://www.paypal.com/cgi-bin/webscr?cmd=_express-checkout&token=xxxxxxxxx&useraction=commit" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:38:19 -0700] "GET /ipn_main_handler.php?type=ec&token=xxxxxxxx&PayerID=xxxxxxxxxHTTP/1.1" 302 - "https://www.paypal.com/webapps/hermes?country.x=US&hermesLoginRedirect=xoon&locale.x=en_US&token=xxxxxxxxxxx&useraction=commit" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:38:20 -0700] "GET /index.php?main_page=checkout_process HTTP/1.1" 503 105 "https://www.paypal.com/webapps/hermes?country.x=US&hermesLoginRedirect=xoon&locale.x=en_US&token=xxxxxxxxx&useraction=commit" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:38:41 -0700] "GET /index.php?main_page=checkout_process HTTP/1.1" 503 105 "https://www.paypal.com/webapps/hermes?country.x=US&hermesLoginRedirect=xoon&locale.x=en_US&token=xxxxxxxxxxx&useraction=commit" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:38:43 -0700] "GET /favicon.ico HTTP/1.1" 200 2131 "https://www.lscoguard.com/index.php?main_page=checkout_process" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:38:51 -0700] "GET /index.php?main_page=account HTTP/1.1" 200 5320 "http://www.lscoguard.com/index.php?main_page=product_info&products_id=101" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:38:51 -0700] "GET /includes/templates/pure_orange_free/buttons/english/button_view.gif HTTP/1.1" 200 849 "https://www.lscoguard.com/index.php?main_page=account" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:39:02 -0700] "GET /index.php?main_page=account_history_info&order_id=4691 HTTP/1.1" 200 5431 "https://www.lscoguard.com/index.php?main_page=account" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:39:42 -0700] "GET /index.php?main_page=account HTTP/1.1" 200 5104 "http://www.lscoguard.com/index.php?main_page=shopping_cart" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:39:42 -0700] "GET /images/no_picture.gif HTTP/1.1" 200 1057 "https://www.lscoguard.com/index.php?main_page=account" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:39:49 -0700] "GET /index.php?main_page=account_history HTTP/1.1" 200 4876 "https://www.lscoguard.com/index.php?main_page=account" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:39:49 -0700] "GET /includes/templates/pure_orange_free/buttons/english/button_back.gif HTTP/1.1" 200 843 "https://www.lscoguard.com/index.php?main_page=account_history" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:39:57 -0700] "GET /index.php?main_page=account_history_info&order_id=4692 HTTP/1.1" 200 5206 "https://www.lscoguard.com/index.php?main_page=account_history" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:41:24 -0700] "GET /index.php?main_page=account_history HTTP/1.1" 200 4879 "https://www.lscoguard.com/index.php?main_page=account_history_info&order_id=4692" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:41:36 -0700] "GET /index.php?main_page=account_history_info&order_id=4692 HTTP/1.1" 200 5218 "https://www.lscoguard.com/index.php?main_page=account_history" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:41:59 -0700] "GET /index.php?main_page=contact_us HTTP/1.1" 200 5043 "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:41:59 -0700] "GET /includes/templates/pure_orange_free/buttons/english/button_send.gif HTTP/1.1" 200 855 "https://www.lscoguard.com/index.php?main_page=contact_us" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:42:12 -0700] "GET /index.php?main_page=account HTTP/1.1" 200 5091 "http://www.lscoguard.com/index.php?main_page=product_info&cPath=0&products_id=126" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:42:12 -0700] "GET /includes/templates/pure_orange_free/jscript/jscript_jquery.js HTTP/1.1" 304 - "https://www.lscoguard.com/index.php?main_page=account" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:43:01 -0700] "GET /index.php?main_page=checkout_shipping&ec_cancel=1&token=xxxxxxxx HTTP/1.1" 302 - "https://www.paypal.com/webapps/hermes?country.x=US&hermesLoginRedirect=xoon&locale.x=en_US&token=xxxxxxxxxxx&useraction=commit" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:43:01 -0700] "GET /index.php?main_page=time_out HTTP/1.1" 200 4689 "https://www.paypal.com/webapps/hermes?country.x=US&hermesLoginRedirect=xoon&locale.x=en_US&token=xxxxxxxxx&useraction=commit" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:43:02 -0700] "GET /includes/templates/pure_orange_free/jscript/jscript_jquery.js HTTP/1.1" 304 - "https://www.lscoguard.com/index.php?main_page=time_out" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:43:08 -0700] "GET /index.php?main_page=account HTTP/1.1" 200 5091 "https://www.lscoguard.com/index.php?main_page=time_out" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:43:21 -0700] "GET /index.php?main_page=account HTTP/1.1" 200 5104 "http://www.lscoguard.com/index.php?main_page=product_info&cPath=0&products_id=124" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"
[17/May/2017:09:43:25 -0700] "GET /index.php?main_page=contact_us HTTP/1.1" 200 5025 "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36"