It sounds like you're trying to record on your internal system drive. Whether it's partitioned to separates or not, this is NOT recommended or supported. You must record audio to an external firewire drive (USB drives are not supported, either).
If it's been working up to this point, you've been lucky.
Also, you can only repair permissions on a disk that has an OS on it. Since your audio partition doesn't have an OS sitting there, you can only verify or repair the catalog of the disk.
Check these guys for good FW drive solutions:
http://eshop.macsales.com/shop/firew...W800_FW400_USB