One possibility:
Check this registry entry:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\ Memory Management\ClearPageFileAtShutdown\ and if the value is "1", try changing it to zero.
(Info)
This setting is created by some security applications to delete the swap file at shutdown. Some (somewhat rare, I think) types of malware have been known to recreate themselves from the swapfile. If the swapfile is large, it can take a few minutes to delete it.