Probably the 3.9 scsi.device, it slows down my A1200/060 as well. Try editing your startup-sequence:
c:setpatch SKIPROMMODULES scsi.device QUIET
Additionaly, Piru's SPEEDYIDE patch from the BlizKick archive adds almost an extra 1 MB/s here, with an IDE-Fix Express. (I could never get IDEFix to work with my CF cards...)