OK, Hopefully I am doing something stupid... I updated to the latest software, and also aquired a Denon 2500 and AVP. Of course neither are in the database yet (no surprise), but I seem to have a problem.
So I decide, since I'm only using about 1/4 of the memory just to add them one at a time. I have been through this twice now, with the same results. I go learn all the commands to buttons (and painfully make sure the names match the function - very time consuming), and download it to the remote (yes I know, should have tested them first). Anyway, several buttons don't work. Worse yet, the IR indicator stays lit for 7 seconds or so (that's odd).
SO I decide, ok I'll just reprogram them. Nope - no go. I can no longer learn any commands for that device (I have not tried the next one yet). I can delete the IR, but when I go to learn, as soon as it sees the data it says failed (it saw the data because it quit early).
I can't seem to get it to relearn anything. Worse yet, the first time I did it, it corrupted some of my existing items (hence leaving them in this time). It's almost like it is corrupted the database of learned commands.

Anyone else seen this, or have any suggestions?

It gets worse. To reload my old working version, I have to initialize the remote to factory defaults. Otherwise it corrupts my other devices (like the TV - it starts doing the 6 second IR transmit, and fails to work).

Yet even more bad :-). Apparently the MSC-400 software has been improved too (I am beginning to regret updating). I tried the above stuff on another computer (same result), and then decided to move to serial. So I am making progress (the serial commands appear to be working - but I have not done the triggers yet). However, now when I add a new serial device and try to name it (using the description), it deletes all previous descriptions (as well as itself). Maddening - sigh.

Hopefully someone else will chime in that it is indeed a SW issue (I write SW for a living), and URC will "quickly" resolve it (since so far I can't use the remote with the new toys :-( ).