I saw a similar post with no real answer, so I'm posting again.
I have an InfoPath form template published to a SharePoint site. On the form, I have on version change set to "Auto upgrade" and it works 99% of the time. However, occassionally, the end user will get the Form Template Conflict prompt and will have to choose to keep or replace the form. I have educated them to always select "replace" however there are some users that still keep. I update the dates on the form each week, so it is necessary that they replace.
Any ideas on what could be causing the form to not auto-upgrade? I have not found any consistency on users getting the prompt, seems to be random.