I think I've already spoken to OP on EAB, but by way of a heads up FastATA Mk-VII definitely *does* work on 3.2. I didn't need to do anything fancy for it to show up and loaded FastATA.driver before prepping and installing.
If it's not detected in Autoconfig the OS is irrelevant: The card isn't initialising, and an autoconfig card will have drivers and tools based on autoconfig initialisation. There's always an outside chance that a specific KS version might stop autoconfig initialising for a card but it'd have to be very weird to not mark the card as disabled, let alone to have an otherwise stable-ish system.
One thing that did lead to general instability (across the board but often resulting in drive corruption) was the combo of my A3660 and ZZ9000. In full HD my ZZ9000 seemed to cause stability problems. I suspect this was the onboard Z3 RAM being used, while the screen and Ethernet were also being used. This happened less on lower resolutions at lower bit depths, but it only stopped when I installed a Cyberstorm (that had on-board RAM of it's own).