after install certain apps can't boot, vfat complaints, system halted

I'm running into this regularly now. I install something new, or update
an existing application, and reboot the system. It gets to loading
windows, then either hangs, or gives me the message, on a blue screen,
that the system cannot find a VFAT component (missing or corrupt) and
the system is "halted". I can get into either safe mode or dos mode
after that. What I've been doing is go into dos mode, run scanreg to
restore a previously started registry, and boot my system. However this
now happened to my palm desktop companion software, which I had updated.
It will not run with the restored registry, but when I re-install it I
can't boot windows. I do not think that this is caused by the palm
package, because I have had these symptoms for many applications, a.o.
wordperfect (although I bought v11 I've gone back to v10 on this
machine) and several others. Sometimes once I have restored the registry
they will run anyway, but not these two.
Does anyone have a better solution than what I've been doing so far?
Thanks in advance.