The only track that can end up with an SBE if you cut it via EAC with a cue sheet is the last track. The time syntax used in cue sheets is always sector aligned.

If the Big Wave File that you are cutting into tracks is not sector aligned itself then the last track will always have an SBE on it. This is the case with CD Wave too. That is why you commonly find sets that have an SBE on the end of each disc. Use shntool to pad the end of the last track.

Perhaps the sector align feature of FLAC can also do it, but I don't know.

Five: I can show you how to use EAC for cutting wave files when I get a bit more free time.