Just my 2 cents, but I get similiar problems all the time, since I edit a lot of video on my system, and many different plugin's and Codec's often screw up my system startup and innevitably the registry.
The program I have learned not to live without is:
"Registry Medic"
www.iomatic.com
Its a little more than a registry program, as it looks at every type of program and dll that has entries in the registry and well as every sort of program that executes or works though the registry.
Its found more than its share of problems with my w2k setup. Including the old easy cd problem. If this doesn't work however, go into this registry entry:
Open up regedt32.exe
hkey_local_machine/Software/Microsoft/Windows/Current Version/
Now look for the directories /Run
/RunOnce
and /RunServices
(Turn on 'View Tree and Data')
One of those directories should have the errant program. Delete the line you find it on, and that should fix it.
Thats if you need to do it without 'registry medic'.