[Five]

FLAC frontend is fine for fixing SBEs. It always moves cues backward, which means that yes, it is normal for samples to be carried over to the following track. Most likely there are also a few samples added to the last track.

get TLH (linked above) and run a len check (under audio file details tab) to make sure that your set has no SBEs and is the correct bitdepth and sample rate.

the wav file should sound identical to the flac file. I'm not sure what you mean by "loss of power"... if your cpu is very weak perhaps you may need to decompress to wav before playing, this most certainly should be identical. I've never heard of anybody having trouble playing back with foobar2000/winamp.