I could be completely wrong, but my guess at the cause would be the registry. Every functionality and feature in Windows has a flag somewhere in the registry. Every query is probably a disk read, and it's a blocking operation of course. Sure, there's probably a cache, but that cache is only so large.

There's a program that I can't recall the name of that can trace registry queries in the program it's attached to. You can attach to basically any process in Windows and see a monstrous number of registry queries.