The problem started after upgrading to Windows 7 AND Pcplus 11. (Simultaneously. Seemed like a good idea at the time

SHORT VERSION: The check input module finds the check reader, initializes it, says "ready to scan" and then never gets any input.
LONG VERSION:
After installing PcPlus 11 on the machine, I downloaded the Magtek Windows 7 driver and successfully installed it. The check reader is a USB "serial emulation" model, so when you plug it in the driver creates a virtual COM port (COM 3) and the computer thinks there is an RS232 check reader connected. This all works great -- I can scan checks into any serial terminal program, and I can change/download/upload settings to the reader from the MICRbase software. In short, the reader is working flawlessly as far as I can tell.
When I open the check scanning module in powerchurch, it finds the reader on COM 3 and initializes it and then says "ready to scan." Yet nothing will appear in the scan field. My guess at this point is that there is some piece of code somewhere that's supposed to take the scanned serial input and copy it into the check number scan field, as if I had done that using the actual keyboard. But since the reader is NOT operating in USB keyboard emulation mode, this critical step never happens for some reason.
Does anyone know why? Thanks so much. In His service, Ian