I seem to remember having the same problem when I used MediaMonkey to rip to FLAC, check out Mark's post on how to get the best from a Squeezebox it will give you some tips on ripping to FLAC using EAC.

www.meridianunplugged.com/cgi-bin/ultimatebb.cgi?ubb=get_topic;f=7;t=000588;p=3#000041

Regards
Gary