I've been encoding using EAC and Lame, and have been occasionally checking the resulting output with mp3utility. The resulting files consistently come up error free (I'd been ripping with other software prior, which generated corrupt files). Once they're ripped, I've been applying album gain with mp3gain, and recently discovered that after that, most of the files exhibit a sych error 99% of the way through the file. Can mp3gain be causing this? Does this compromise the long-term integrity of the file? Undoing the gain changes does not seem to remove the synch error. Has anyone else experienced this or know anything about it?

It's probably the mp3gain tag data that mp3gain writes at the end of the file. If you decode such a file with mad CLI for example, it will say 'loss of synchronization' right at the end but doesn't print this if tag-writing is disabled. If this is the case then it shouldn't be a problem.

You mean if tag-writing is disabled in mp3gain? I guess the only other consequence of that would be that you couldn't automatically have mp3gain undo the changes it made to the file. I'll try it and see if the problem disappears by disabling tag-writing in mp3gain... Thanks.

Ok - as a follow up:

I ran mp3gain twice on two copies of the same file (which showed no errors when first analyzed with mp3utility):
After processing with mp3gain writing tag info to it, mp3utility detected a synch error at the very end of the file.
After processing with mp3gain NOT writing any tag info to it, it came up error-free.

Guess that answers it.