Here's a waveform picture of how foobar 0.7.7b (don't know if older versions have this same problem) incorrectly decodes a flac + cue combo to separate wavs. In the picture you see merged two adjacent decoded wavs (taken from a mixed compilation). The marker shows where the first file ends. As you can clearly see there's a part that's decoded twice - once at the end of the first wav and again at the beginning of the second wav. Playback of the source flac file in foobar is just fine.
I tried to decode several times with reboots and clean foobar reinstall between atempts to rule out any windows foolishness and the result was always the same. No DSP or anything in foobar turned on while decoding - just plain conversion to 44.1 khz wavs.
Just tested... 0.7.6 behaves in the same way.