I've had this problem for about 4 or 5 years now, but today was the first day I procrastinated long enough to figure out what was going on.
I occasionally noticed that certain songs on my rockbox'd Sansa Clip Zip with track-level replaygain enabled would be significantly quieter than the rest.
To sum up a long story, the replaygain tags are not added correctly to tracks that are converted (in my case, from FLAC) to mp3 during handheld sync. After I sync the Clip Zip and open the tracks on the player using foobar2000's tag editor, all of the songs that have been converted during the sync process are missing the replaygain_track_gain tag that foobar2000 (and I assume Rockbox) uses to grab replaygain info. However, all of the metadata volume tags that MC writes, such as VOLUME LEVEL (REPLAYGAIN) are present in all of the files. So it seems that the following tags are not copied to the converted track during handheld sync even though they are created correctly for the original files via MC's audio analysis:
replaygain_track_gain
replaygain_track_peak
replaygain_album_gain
replaygain_album_peak
It appears that rockbox uses these tags for replaygain info and not the:
VOLUME LEVEL (REPLAYGAIN)
tag that is correctly written to the converted file.
You can see in the attached photo the tag properties of two songs on my Sansa Clip. The song on the left was synced as an mp3 and the song on the right was converted from flac to mp3 during the handheld sync. The replaygain tags are not present in the converted song.