The simple fix for this should be to boot the original firmware (assuming it is expecting the original firmware to respond in some fashion), as my guess would be that it (quite rightly) doesn't expect there to be a third party operating system on a closed platform.
A simpler fix for this still (assuming you don't use the original firmware), would be to simply not use any form of sync management software at all - especially not any that wants to use the crazy iTunes media obfuscation scheme* - as it is absolutely, completely, and totally unnecessary for Rockbox.
This is often viewed as one of the major benefits of Rockbox. it requires no media management software whatsoever. Just drag and drop your files anywhere in the device storage (except /.rockbox), and you will have access to it via the File Browser or Database (though the Database is only ever going to be as useful as the metadata is complete).
[Saint]
*Note: If you have previously synced music to the device via iTunes, this pretty much forces the use of the Database because iTunes likes to obfuscate the files and scatter them about the storage volume in seemingly random order, because they apparently wanted to be as annoying as possible in their quest against the dirty, dirty pirates. Personally, I would remove this (just format the storage volume if you have your media backed up, nothing important lives in the filesystem that the original firmware won't replace on the next boot) and start afresh using drag and drop and order the media on your device however you want to.