The quickest way to check is to do what you suggested, return the msconfig Startup entries to what they were before you amended them, then shut down and see if the slow shut down has been solved.
If so, then you can check which entry makes the difference by one by one, removing a tick to one of the entries you removed originally, then shut down after each change.
It's laborious but if the change in the msconfig did slow your shut down speed, this way will find the entry and you can then do some more research on why.
If returning msconfig to the way it was does not return the shut down to normal speed then we must think some more.
I am running XP 2 Dell 4700 Pentium 4 3.2GHz 1G Ram. The machine has run smoothly until yesterday. I tweaked the msconfig a bit to uncheck some files that were loading at startup. I was very careful to double check if a file was needed. If in doubt, I left it checked. The machine starts up fine, but now there is a noticeable lag in shutting down. It takes a longer time than usual for the screen the pop up that lets me click Shut Down or Restart. I ran check disk, clean disk, and defrag (which told me I did not need to defrag). In a pinch, I can always restore back to a time before I started "tweaking," but thought I would post the question here to see if anyone has any good ideas what might be going on. Thanks. Jane