Do you have a CUE sheet for the WAV file? If so, you can go into EAC and choose Tools, Split WAV by CUE sheet to get individual WAV files, then convert these to FLAC individually. If your player supports gapless playback, you'll still get smooth transitions between tracks on such things as live albums where the music runs together.
The only way I know of to make a CUE sheet in EAC is with a CD as source.
I can't seem to find a freeware CUE sheet creator that can pull the info out of WAV files, but this page has some directions about how to make one using only a text editor if you know the track timings.
I found the way to automate the process of making separate tracks from the one big file within Audition.
Saving them as .flac with the audition plugin even keeps the metadata and BWF which is exactly what I want.
The way to achieve this is covered here: http://www.adobeforums.com/webx/.2ccd622a/2