Pretty sure I've encountered that, though I've encountered so many different glitches and errors in the eleventy-zillion times I've installed Rockbox (on flash modded ipods, which are a lot more temperamental than the original hard-drive) I can't remember when they happened and what fixed each of them. With that one, I _think_ I just did what the RBinstall utility instructions suggested - manually rebooted the ipod at that point.
What I vaguely remember helped was to manually reboot it into either disk mode (holding centre and play button after holding centre and menu button to reboot) or into original firmware mode (holding menu button alone for a while, after rebooting) rather than letting it boot into RB's usb mode (which it's supposed to use for installing RB, but at least on flash mods doesn't always work). Messing around with windows formatting things usually causes more problems than it solves.
However these sorts of problems always occurred with flash mods (which are a PITA, really), if it happens with the original hard drive that suggests maybe something else has gone awry (a failing drive?).
I'm not an RB developer, though, so maybe someone will come along with a better solution, but it does _tell_ you to 'try and remount it manually', so seems logical to try that first.