Looks like the disk from the Amiga hardware database is slightly newer than what I have... that's good. But keep checking what the installer did - it may have messed with your startup-sequence - and review the readme. I think amiquest.device is still kicking around somewhere in there, possibly in the ROM of the PCMCIA adapter (Scout or SysInfo will tell you if it's active). A different device and filesystem seem to be used depending on whether you're doing CD32 emulation or not. See the install disk's Devs/DOSDrivers/CD0 vs. Storage/DOSDrivers/CD0.
Bottom line, I found that it works alright on a more or less stock system, but if there's anything nonstandard about your OS installation (before or after you install) then something breaks. I recommend a manual installation.