CompuServe Messages

I've got a problem with a Toshiba 3401 connected to a Future Domain TMC-850M (there are no other devices on the SCSI card) One of the ways that the problem manifests itself is that if I do a DIR from DOS I only see 1 directory when I know that there are others (because they are shown within my Hard Disk Manager and I can do a CD to the other directories from DOS). I thought at first it may be something to do with having >16Mb of RAM but I've reduced my system to 8Mb and the prob. persists. I have checked the termination on both the drive and card and it seems OK. It has worked in the past and the only change I can think of is that I had to reset by CMOS settings back to the factory defaults within the BIOS set up program. Has anyone any suggestions? Just for Info it is running on DOS 5.0, EMM386 (with exclusions for the SCSI card memory area), a Peak 386/33 mother board, Sound Blaster Pro 16, 2 x IDE drives, MSCDEX 2.17.