No clue either, but sharing your first suspicion that it might have to do with your recent shortcut changes... Does the error console show anything interesting after startup? Did you restart the system again? And what happens when you start a complete, fresh unzipped portable version?
The issue started long after I had made the last changes to my accel.cfg. The shortcuts had been working fine until then. As for the error console, I can't make head or tail out of that stuff, but I don't see anything relating to shortcut keys. At first I suspected that one of my newest macros might be doing this, although they all work perfectly.
Yes, I rebooted the computer, too. That was one of my first thoughts, because it has cleared up some weird behavior in the past.
As I mentioned earlier, I did try replacing the files in KM's root folder with a fresh copy of the portable version, thinking that maybe one of the program files had been corrupted, and also restored my profile from a backup copy on an external hard drive, but it made no difference.
The Ctrl key itself is still fully functional in K-Meleon, as long as I only combine it with A to Z or 0 to 9. It's beyond me why those VK key combinations are being singled out, especially when they work in other programs, and Alt works fine with the VK keys, even in K-Meleon. Someday I'm bound to discover the cause quite by accident, but meanwhile I've redefined the faulty shortcuts.
Using KM 75.0 on Windows 7 (x86)