You might be best to use something like Process Explorer or Process Monitor from Microsoft and start digging into the system to see what processes are locking on what. Is a process hanging on a registry entry, a permissions issue, a file locking problem.
I use Process Monitor quite heavily for troubleshooting application problems through my IT job. It will tell you everything a process is trying to do when opening, running, closing from opening files, accessing registry entries etc. It can be quite daunting to use at first, but once you figure out filtering options and start looking you might just stumble on what is causing the problem.
If I get time I'll have a look at my system later on and see if I can write a quick how-to that might point you in the right direction. Thought I would just mention it quickly to get you started.
EDIT: Found some resources to help with using Process Explorer:
http://www.howtogeek.com/...rnals-pro/lesson3/all/http://www.howtogeek.com/...rnals-pro/lesson5/all/