Im pretty sure the marketing spill for the ISA XT CF card you got, mentions that it can co-exist with MFM/RLL controller cards. It has a large selection of different addresses for this purpose.
Edit - Ive still have a full height 5.25" MFM drive in my parents garage. Sounds like a jet taking off. THink it has a bad sector towards the end of the drive, since on my a500 it would corrupt at the exact same % full.