How To Diagnose Your PC with a Clean Boot

A clean boot in Vista is performed in very nearly the same way as in XP. You start by entering “msconfig” into the Start Search Bar in the Start menu, which will launch the System Configuration Utility. In the System Configuration Utility, click the “Selective Startup” radial button and uncheck the “Load Startup Items” option.
Go to the Services tab, select “Hide All Microsoft Services” and press the “Disable All” button. Click OK. Reboot as requested and see if the problem goes away. If it does, you know the services are probably the issue.
You probably disabled a whole fistful of services, and most of those are likely doing something worthwhile, so now we’ll need to narrow it down to just one culprit. First, we’ll divide the field by manually re-enabling half the services in the System Configuration Utility and rebooting.
See if the problem goes away. If the problem still occurs, then one of the programs you just enabled is the perpetrator. Otherwise, it’s one of the other half of the programs. Either way, you’ve eliminated fifty percent of the services as potential trouble makers. Now, change the list so that only half of the suspect services are enabled and repeat the process.
After a couple iterations of this halving process, you should be able to pinpoint the program that’s causing your problem. You’ll have to decide how you want to resolve the issue. If the interfering service is something you know you can live without, you can go ahead and disable it from the System Configuration Utility’s “Services” or “Startup” tabs, depending on the program.

If it’s something you want to keep, you’ll need to figure out some way to resolve the conflict. This can be easier said than done, but a good place to start is with a Google search for the interaction, or by visiting the conflicting programs’ forums, if they have them, or contacting their support departments. Good luck!