WAV+CUE sheet, converting to FLAC with embedded cue.
After conversion, foobar hangs. FLAC file is generated, but no tags inside,
after killing and restarting foobar.
converting without cue works.
manually embedding cue works, but foobar misses titles from cue, displaying
album title on every track.

all above works fine if I use Monkey Audio.

Actually you need more patience

FLAC uses a tagging format which is not written to the end of file, so the whole file needs to be rewritten while embedding the cuesheet. Writing everything to a temporary file and back needs some time - just wait a little bit.

WavPack doesn't have these kind of problems, because it uses APEv2 tags which are located at the end of the file.