The achilles heel of the empeg has always been the difficulty and time it takes to get stuff into the darned thing. The v3alpha firmwares merely make this slightly more troublesome than usual.
When I was actively loading tunes onto my own players, I wrote some Linux scripts to do it using emptool, just to avoid the whole need to feed and care for a GUI.
But I don't think those scripts work anymore, so lately I've been using Emplode inside a win98/VMware session to adjust things. Seems to work, even on v3alpha.
Cheers