Well, EAC has been in beta for a while, it's expected to see a few bugs now and again. Make sure you've installed the latest flac codec from here.
Also here's how my External Compression tab looks like, maybe it helps:

The Additional command-line options writes:
Code:
-8 -V -T "ARTIST=%a" -T "TITLE=%t" -T "ALBUM=%g" -T "DATE=%y" -T "TRACKNUMBER=%n" -T "TOTALTRACKS=%x" -T "GENRE=%m" -T "ALBUMARTIST=%v" -T "ALBUM ARTIST=%v" -T "COMMENT=EAC Secure Mode, Test & Copy, AccurateRip, FLAC -8" %s
(I'm pretty sure it doesn't need to be exactly that for it to work, it was just a requirement for Pedro's uploaders)