By "potentially faulty," I mean the issue of my computer not booting correctly because the hard drive will suddenly spawn a DH0.1 and a DH1.1 alongside DH0 and DH1 when I install the 3.2 roms, and goes back to normal (just DH0 and DH1) when I reinstall the 3.0 roms. I've upgraded WB roms in the past (1.2 to 1.3 to 2.04 in my old Amiga 500), and that never happened before.
What your describing, happens when using a certain version of SFS for partition. So what Filesystem are you using?