All versions of Rockbox (but less so the most recent development versions) have problems with writing to iFlash storage. Something to do with the ATA driver not being written with that kind of storage in mind, so the timings are not right, or something, I gather. Shows up when syncing tracks to it - if you do it with the device in rockbox mode it tends to make errors, sometimes very obvious, causing skipping and other problems with playback, or even a corrupted file system, sometimes it seems more subtle only showing up if you do a hashing/fingerprint comparison between the tracks before-and-after writing to the ipod. Also can show up when you try to create the database, because that also involves writing to the drive. That's why I build the database with the simulator on the PC.
Personally I found fewer problems with the quad than with the dual iFlash.
RB devs did some work on it recently, hence the post-point-release versions apparently perform better in that regard.