If I remember correctly, there is a 4gb or 18 minute limit for .avi files on a FAT32 drive. This is not the case if your drive is formatted to NTFS.
One alternative for you is to use the Scene Detect setting in Capture and that will break your clips up - drop all these unedited clips back onto the timeline and chose File > Export > Tape and re-record all your footage onto another DV Tape. Whilst it's not a backup on a disk, it's a copy of your tape.
Canon HV30 | RODE VideoMic | Adobe Premiere Pro CS4.