Now according to the "official" changelog, all the 3.99 changes have been fairly few and trivial. Who actually knows when that was updated though? It had to have been a while ago because there's been well over 250 patches land according to the CVS activity stats, and something has obviously changed regarding bitrate and therefore probably quality of the file, though it's only a 5-10% reduction in overall bitrate in any given file and I'd be hard pressed to spot one or the other except that the one encoded by Lame 3.99 is smaller.
I was wondering if anyone more "in the know" could shine some light on why it is doing this and any possible impact on quality it may have.