A spyware/adware scan might be in order before you do anything hasty. On top of that, some applications have known problems with being launched at startup. They halt and effectively manage to pause the entire startup process. Among the offenders that I know of are some of the newer Symantec antivirus packages (Doesn't cause the pause regularly, the majority of the time they'll load fine, but every now and then there are problems).
If a few system scans (I'd recommend scanning with at least adaware, spybot, and an antivirus package [such as AVG]), don't resolve the problem the next thing I'd say to try would be:
1. Next time the machine boots correctly go to start, run (Or press the windows key + the 'R' key on your keyboard at the same time)
2. In the box that comes up, type msconfig
3. Click the startup tab and have a look at the list of programs launching when you boot your machine. If there's anything there that you don't want to load, untick the box and click apply. Make sure that you don't untick anything you can't identify, as some processes are required to keep things like antivirus, sound, graphics cards, working as they do
4. If there's anything you can't identify, googling the name will often yield results which tell you what it is and whether or not it is critical. Failing that, you could try posting them here to see if anyone can help out with them
Depending on what's causing the problem that may or may not be useful, if it still doesn't help, like some of the others have said, some more information such as system specs and the applications which you have running on startup might help.
