I too have a problem with using Simple SEO URL mod with PayPal IPN. Looks like the money gets transferred, but no order confirmation emails to the buyer or merchant from ZenCart. Confirmation emails from Paypal does get to buyer and seller. And the order does not show up on admin interface. The record does show in the IPN records (if you look there).
One syptom of the problem is that
http://www.example.com/ipn_main_handler.php is coming up blank page as oppose to saying "Nothing to process. Please return to home page." (as it supposed to in 1.3.8)
So, I had removed the mod by ...
To remove SEO URL module, I did the following...
1. Remove the mod re-write code from .htaccess
2. Remove these lines from includes/functions/html_output.php. Do NOT remove the file.
//bof simple seo url
global $ssu;
if(($link = $ssu->ssu_link($page, $parameters, $connection, $add_session_id, $search_engine_safe, $static, $use_dir_ws_catalog))!= false) return $link;
//eof simple seo url
2. You can remove all the other files that you have uploaded for the modules. And can remove the "admin/includes/module_installation" folder and "admin/includes/templates" folder if you don't have any other things in it.
3. Remove table links_aliases (if not using for anything else)
4. If you are also removing "module manager module" you can remove table module_version_tracker
5. Remove records with the following keys from configuration table:
SSU_ID_DELIMITER, SSU_MAX_LEVEL, SSU_EXCLUDE_LIST, SSU_LINK_ALIAS,
SSU_MINIMUM_WORD_LENGTH, SSU_MAX_NAME_LENGTH.
6. Remove the record with the values "Simple SEO URL" from configuration_group table.
The removal sequence worked for me.