Is there a known occasional glitch with the RAM buffering algorithm? Sporadic wackiness in the D/A converter? Have others experienced this?

No, there should be no odd clicks or pops during playback unless there's something wrong with the MP3 file to begin with.

Do a RAM test as described here if you can.

There is also the possibility that the clicking problem is happening somewhere in the amp/speaker system and has nothing to do with the empeg (although I'm sure you've checked that, too, right?).