Having recently reprogrammed my AV3000 to accept commands from an Arcam AVP700 pre-amp I had constant remote freezes (usually during volume up, down or mute). I found it would freeze and constantly send a command. After reprogramming it about a half dozen times I played with the length of time I held the button on the Arcam remote (Ron Aronson mentioned this earlier in the thread). This solved the problem for me.
There are trade-offs with this solution. Namely, I can no longer hold the volume buttons on the AV3000 and have a continuous command send to the pre-amp. This results in multiple presses to control the volume. The benefit is the remote no longer freezes. I believe this problem is device specific as I've never encountered any issues on any other devices. For what it's worth the Arcam unit comes with a CR80 universal remote. So the AV3000 was actually learning from a universal remote.
I assume this solution will work for the 3100 as well.