Have you tried booting in Safe Mode? If the problem goes away, something loading at normal boot-up is the problem.
In that case, open msconfig and go to Startup tab. Uncheck everything except items related to your antiviral suite and firewall. Reboot and put check in "Don't show this again' box, if it appears after you reboot. If the problem goes away, you can go back into msconfig and re-check items one, or a few, at a time, rebooting and checking that box each time, until you ID the problem.
If unchecking everything except antiviral and firewall in msconfig doesn't help, disconnect the network/modem cable so you're off then net and uncheck everything including antiviral suite and firewall, and then reboot. If that fixes it, your antivral suite is the likely cause.
BTW: Have you disabled Windows Indexing Service? This useless hog indexes the hard drive in the background so searches go faster, but it's well-known to cause the types of hesitation you're seeing. And the larger the hard drive(s), the longer the hiccup.
Is your browser or Outlook, Thunderbird, or some other mail service automatically checking for new mail every so often which might be causing things to hesitate?
Is some other app (eg, Adobe Reader, Adobe Flash, iTunes, QuickTime, Java Updater, etc) set to phone home every so often looking for updates? Any of those might be the cause but they won't show up in the Scheduler. You should be able tell that after you uncheck them in msconfig.