It sounds like you have learned a “dirty” command. This happens sometimes, and freezes up the remote so it won’t learn anything, just as yours did. Clear the component key (not one key at a time, but as follows; for good luck, do it twice) and try again. Sometimes it will not happen again so you can learn all the commands, but sometimes it will. If it does it again, note which Bose key caused it, and stay away from that key.

Commander off/Muting
Set
Reset
Compo
Press the component key you want to clear (AMP)
Yes
Hold Commander off until the remote turns off

If the volume keys repeated on the original remote (which I know they did), then they should repeat on the 3000.