My player suffers this 'lag' as well, about once a week. Typically it occurs just after I pause the player - shut off the vehicle - start the vehicle allowing the player to boot. Then when I un-pause the track I get exactly what you described. A blip of music, a pause, then it resumes and all is well. I'll have to verify this but I seem to recall seeing the battery icon when it happens. Not sure though.

I can't consistently reproduce the behavior and my backup player doesn't seem to do this at all. The backup player is hardly ever used in the vehicle though.

My player started life as 1.03. It's now 2.01 and running Hijack 455 (I know, I need to update.) I have telnetd and rsync installed. No extra memory but I do have a eutronix light kit.

Sorry I don't have any insight as to the cause. But you're not alone.