So this is just to wrap up this post for others with similar issues. It turns out that sometimes it's the scanner. After several different computers, several different cables, several different scanner programs, and trying every COM port and driver setting combination possible, the only thing left was a problem with the scanner.
I've had amazing support from Nick, the creator of Scan125 and Scan75. He provided custom versions of his software that logged extra information to troubleshoot the problem. The results were erratic answers from the scanner and no conclusive results. We both agree that it must be the scanner. Maybe a bad memory chip, bad firmware (non-upgradable), bad "something-or-other"... but with everything else ruled out, it is the scanner.
It took about 20 minutes to manually program the scanner with 60 frequencies. Sometimes you just need cut your losses and admit defeat.
Thank you Nick for all of your hours of help and correspondence! Hopefully this thread will help others in the same situation.
Edd