Using Foobar2000, I converted a few of my FLACS to MP3 format via Diskwriter and Lame 3.96.1 (alt preset standard) then replaygained the mp3 files, each track resulting in a Replaygain track value of .01 db less than the FLAC files. I also tried the files at the insane profile, which still give .01 db less. I am guessing that the differentiations are due to added noise from encoding? Perhaps frames getting removed/padded?

Converting using a lossy codec will often result in a difference in replaygain values, since the lossy file does not contain the same audio data as the lossless file. Instead the lossy file contains audio data that is perceptually similar to the lossless file.