Hi Bilbee,
Here is something for you to try.
When you are in windows press ctrl-alt & del together it brings up the CLOSE PROGRAM menu..
Look to see if any are not reponding..
I all clear then select the top file and select Close, then shutdown your system.
if it closes down ok then that is the offending program which is halting the system on shut down. If not select the next and so on,, DONT select Explorer this wont close.
dependant on what is is you can disable it in the startup sequence which is
START/PROGRAMS/ACCESSORIES/SYSTEM TOOLS/SYSTEM INFORMATION
Look under the menus and find the startup and edit it, disabling the offending prog..
I have also found that using certain cdr writing software can also cause this. And a little program that comes with some budget a4 scanners called WATCH.EXE all this does is wait for you to lift the scanner lid..get rid..
The other solution is a fresh installation and monitor when it starts misbehaving install each program on there own then run it for a while..Thus trcking down the program.