I had a similar problem as well. I confirmed that it happend both during the day and at night, and I also used another remote with it (Palm V running OmniRemote). It only happened about 4 or 5 times during the last year, so it's certainly not as bad as your case.
I ended up sending mine back to empeg to replace the IR receiver. The had it fixed and sent back to me in a couple of days.
-Trevor
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Mk 2, Green 12GB 080000349
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-Trevor
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Mk 2, Green 12GB, Tuner, 2.0b11, 080000349