When I get issues like this I always reach for Sysinternals Suite ProcMon.
The first time one uses it, it is painful; but the more you use it the more you might want to use it for other purposes.
You need to learn how to filter out stuff, because you will see something like 20,000 system calls per second.
Then you begin to see why Windows runs so slowly. There may be a few thousand calls just to find a file name.