I have also had the same problem described here with the remote - it began to appear a few months ago. I've been through a few batteries already, and like the FAQ entry indicates, when the remote started to become "flaky", I replaced the battery. So, a few months ago, when it became flaky again, I replaced the battery, but it still continued to act flaky with a brand new battery. Furthermore, I took out my brand new remote that goes to my backup Empeg and put a new battery in it - and it too was flaky for a while.
I'm not operating in direct sunlight. I've noticed that removing and replacing the battery would sometimes remedy the situation - albeit temporarily. I'm at v2.0b13 - so it isn't that input lock problem either. It started getting so annoying that I rarely use the remote anymore.
My next line of troubleshooting was to get one of my old/spare/orphaned remote and configure the Empeg (using Hijack) to respond to it, then see if the problem also exists with a completely different remote.
To be honest I've never really liked the remote that came with the empeg - I don't like the tactile response of the buttons - so I've been in search of a replacement, something that offers an actual button that depresses.
I'm going to try to bend the contacts though... I was actually about to post about this problem to see if others were experiencing this problem too
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BleachLPB
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NewFace MK2a