Just thought id let everyone know ive managed to solve this finally! All i needed to do was install IDEFix97. It sorts out the problem for both os 3.1 & 3.9.
tbh, i had assumed that installing os 3.9 on its own would be enough to sort out any problems with IDE interface, but clearly i was wrong 
Just managed to shift 1gb of data between partitons on the drive where as before i could not manage a whole floppy before the system crashed.
I think i will have to register IDEfix if its still possible.
I'm having a similar problem where my fast memory isn't showing up. The hard drive is all there however.
I will have to try this IDE Fix and see if it helps.
