My company has just changed the order processing software we are using and it's causing some issues with Google Analytics conversion funnel tracking. Specifically, there is one point in the funnel where making certain selections (which about half the people do) causes the page to reload. Also, on the login/register page, if they miss a field, the software tells them missed the field, but loads a new page which has a different URL which is not a part of the funnel when a mistake like that isn't made.
All of this is causing Google Analytics to report people as leaving the conversion funnel when they really haven't. About a third of the traffic is being shown as exiting the funnel with the exit URL being the exact same URL as the step they are supposedly exiting from (example: the visitor enters on page1, moves to page2, Google is showing that they exit on page2 and go to...page2.
Does anyone have any suggestions of how to deal with this in Google Analytics? If not, do you have a recommendation of an alternative analytics program which can deal with the situations mentioned above?
PS - Changing the way the checkout software works does not appear to be a viable option.