It depends on what you are monitoring, but cryptographic hashes should not change from a simple reboot.   The exception to this are the dozens of files that do get touched when Windows boots.   

It would help to know where files you are monitoring, but Windows update does replace certain system files on your hard drive.  That's what a patch does.  Since the contents of the files have change, the hash will be different.  When the contents change, the hashes changes.   That's the purpose of a cryptographic hash algorithm. 

http://en.wikipedia.org/wiki/Cryptographic_hash_function