Oh dear, my poor boy :) I had a E-105, and the normal build was already damn slow! So if I can make a suggestion, forget about the official MAMECE build, and get Darren's E-1xx build from there. :)
It's lighter too, so I guess that you shouldn't have the same problem.
also, you've got a CompactFlash card right? I highly recommend you to have one and put all your roms in the "MAMECE" directory at the root of the CompactFlash card (I'm not sure about the name of the directory, but it should be something similar and in the root of the card). That might also be your problem.
Old Japanese saying: Monitors may still work with a dead cap, but they will not withstand a shotgun shell after I fall in the crocodile pit in Shadow Dancer 20 times in a row.