XDelusion, is your MaxTransfer speed for the CF card partitions set to 0x1FE00 ? If it's not, it's possible that could be the cause of some of your problems. Change it to that in HDToolBox (if it's not already) and try it.
I am running into the same problem. The only thing is when I set MaxTransfer it keeps defaulting to 0xffffff. Its like the setting does not stick...
A1200 - GVP 030/40 with 32mb ram.
Thanks.