When I took the MX-3000 out of the charging cradle, all of the hard buttons were backlit and the remote was locked. In the past, if the remote ever got into a messed up situation, I simply pulled the battery power, waited, reapplied power and I was good to go.
So I tried that this time and the backlighting was fixed and the remote was responsive. However, I find that the up/down/left/right arrow hard buttons no longer issue the correct commands. As an example, the up arrow that is programmed to scroll through menus within the cable box, now mutes my receiver! The other three are messed up also and send incorrect commands.
So I tried pulling power again, but it didn't help. Then I hooked it up to the computer to reload the programming into the remote. It still didn't work properly. Strangely enough, if I leave the remote connected to the computer and use the MX3000 editing program to send a test signal for those buttons, it works correctly.
So then I thought I'd go to the setup screen in the remote and do a reset to the factory defaults. I can use the up/down/left/right buttons to move around the system screen in the remote and am able to reset to factory defaults. Then I reloaded the remote with my programming and it still doesn't work right!
I am totally stumped with this one. Anyone have any ideas what might be wrong?

Sounds like your file is corrupted. You might want to try doing a factory reset and just redoing a single device and testing that to see what happens.