Digibooster and Octamed use AHI!? I thought you needed the Maestrix installed to access AHI on those programs! :-o
Also there is a ROM patcher built in to AmigaOS 3.9 so it will have to load in a custom ROM image based on KS3.1 on your accelerator card. It's possible that you're only getting 3.1 in your card and not getting 3.9's ROM image based on the way you're doing it.