My bet is it is trying to read a drive that isnt there.
Usually when there is a long delay at that point windows is
looking for a floppy drive or CD that may not even be there.
Installing the iPod probably upset the house of cards that
is the windows registry.
Looking at the task list for the one pegged at 100% cpu
is a good idea, but I'll bet it will be EXPLORER.EXE.
Anyway- check your drive assignents when My Computer
finally opens and look for something that dont belong.