Are you saying that the iPod switches to Disk Mode and then the computer doesn't see it properly? If that's the case then it's nothing to do with Rockbox since that's Apple's software. iTunes should be able to see an iPod that is in Disk Mode. Also, your Mac should recognize it as at least a USB mass storage (UMS) device.
Something you say sounds strange. When you say it charges it, do you mean that Rockbox is still running or that it charges while in Disk Mode? Clarify please.