I'm not at all sure whether this is related, but I thought I'd share this.
We had one person that was a little quick to swipe the credit card. She'd swipe it before the appropriate window was quite open. It would cause the credit card window to go into the background (behind the program), and gray out the part of the program that was still visible. We solved this by getting her to slow down a little and wait for the window to open completely.
It's similar when I'm generating reports. If I'm printing to pdf, for instance, and there's a file already with that name, the program will come up with a "do you want to overwrite existing file" window. However, that pop-up window stays in the background (behind the program), and the program remains grayed out until it's addressed.
Part of the reason that these were difficult to figure out is because we have the Windows taskbar disappear so it doesn't get in the way of the EZP Sales Window. When the taskbar is visible, it's easy to see that something is waiting to be done.
However, I don't recall whether the problem with the credit card window showed anything on the taskbar. I found that I could just drag the EZP main window off to the side, revealing the credit card pop-up window.
Is it possible that the pop-up boxes referred are hidden behind the rest of EZP?