Well, found my solution.

Of course, I feel like a little silly that I didn't figure it out sooner.
This post for Simple Google Analytics helped:
http://www.zen-cart.com/forum/showpo...postcount=1462
Yes, indeed, it interferes with pop-ups.
So they put in some exceptions to the code so that it wouldn't mess up the popup windows:
Code:
if (in_array($current_page_base,explode(",",'popup_image,popup_image_additional,popup_cvv_help,popup_coupon_help,popup_attributes_qty_prices,popup_search_help,popup_shipping_estimator')) ) {
Of course, the print invoice addon isn't installed on everyone's site.
So, I just needed to add it into the exceptions:
Code:
if (in_array($current_page_base,explode(",",'popup_image,popup_image_additional,popup_cvv_help,popup_coupon_help,popup_attributes_qty_prices,popup_search_help,popup_shipping_estimator,popup_print_invoice')) ) {
That was it.
Pretty easy. Too bad it took me all day.
Cheers.
Jason