So what's the problem here? If it's fixed in 3.98.2, I don't understand the purpose of this thread.
Addendum: I just took a quick look at the MP3 frame heaers. They are correct (they all report 44kHz). But LAME switching (internally) from 44kHz to 48kHz would account for the discrepancy in track duration, pretty much. I'll try to get you the source material.