Yeah, i'd say it's a temp file thing, if i had to guess. maybe in a situation like that, there needs to be an old copy and a new one in the same temp file. with each 1.23 GB, there you go.
Just a shot in the dark, there.
FWIW, EAC is frowned upon not because of anything wrong with EAC but because it signifies that a show has been expanded from shn or written as audio from wav and then converted back again.
(One more note: now that you have EAC working, you can read about offsets and get that figured out. It isn't totally necessary, but the real hard-cores figure that out. then they can take a shn, expand it, burn it, rip it back to wav, shn it again and get the same md5 files. it's not easy to do.)
good luck, make sure you have all your firmware updates.
UJ