I had the same problem of not being able to receive payment on a customer's job. What I discovered is that you need to click on the "Customers" tab, go up to "View" at the top of the screen and select "Re-sort List".

Somewhere along the way our bookkeeper may have clicked on that to re-sort the list for her entry needs. When I went in the next day I was not able to apply payment because the "Jobs" in the list got resorted alphabetically and that system could not find them. Once I re-sorted it back then the system was able to accept the payment correctly.

You have to have the system in single user mode to do that.

I hope this helps.