There actually is a bug with respect to VBR in all released versions of lame, including the one you're using. It's fixed in CVS, but it may be easier to use another utility to fix the files. I know for a fact that Mark Lord's mp3tool does the right thing, if you can get a binary for your OS. I'm sure others also work, but I don't know which ones. I know some definitely do not, and will actually end up truncating your mp3s.

IIRC, there was also a bug in the empeg player software in regards to MPEG-2.5 and seeking, but that may not be your problem, as I think you're not using 2.5 anymore, since you say you resampled to 44100, and that frequency is only available in standard MPEG-1 mp3s. But I could be wrong about any part of that.