I'm running Rockbox v3.13 on an iPod 3G updated with a 1300mah battery & 80gig Toshiba drive & was unable to locate an answer for this...
In Apple mode, Sound Check works fine on normalizing the volume of everything, but, in Rockbox, Replaygain normalization only works on mp3s--all of my ALACs (16/44 or 24/48 - converted from CDs with the current version of dbpoweramp) play at widely varying volume levels.
I've been through the Replaygain settings, but didn't see anything that references file format. I've also been through the Sound & Playback settings and didn't see anything there either.