I'm having the exact same problem. My COM port is a real one, not a USB/Virtual.
I have no problem at all running ProScan or other software that talks to the scanner.
Also, after the program quits, the scanner display is blank and blue. Power cycling the scanner brings it back to life but the firmware was not updated.
Yep, same thing here with the scanner going blue and being blank. Here's what solved the problem. Use the USB cable that came with the scanner. Evidently, the Uniden software will not work with a real COM port for whatever reason. You gotta use the USB cable to do the upgrade. I was able to upgrade the scanner that way. So try the USB cable.
I prefer using the COM port on the back of the scanner with ProScan so as to avoid having a cord sticking out the front of the scanner that somewhat gets in the way of using the knob.