This seems to be a long-running issue. I have decided, like many others, to keep master copies of CDs and vinyls in FLAC with cue sheets. Amongst other advantages, this means I can play the whole flac file "gapless" by just ignoring the cue sheet.
I have, however, found issues with playing individual tracks. VLC doesn't find the right place in the file, but appears to be rounding down the position in the cue sheet to the nearest second. Normally, this doesn't matter as there is typically at least a couple of seconds quiet between tracks, but it matters if there is no gap. Example: Carmina Burana, Chicago SO, Levine last track is indexed at 59:17:50 (3557.67 seconds) but VLC starts it at 3557.0. The transition from the previous track sounds horrible. Could someone have a look at the conversion?
It appears gapless playing between two tracks stored as separate files is not coming to vlc anytime soon, but why can't vlc recognize consecutive tracks to be played from a cue sheet and just let the player run through? It shouldn't require any fancy programming.
Just a suggestion......
[using 2.1.3 on Win7 64-bit]