Does the hard drive spin down at any other unexpected times? Do you actually hear it spin down then back up, or is there just an apparent freeze of all activity, then suddenly a rush of hard drive activity?
I'd suggest these temporary changes, one at a time, to see if the problem is hardware related, caused by power settings, or services interactions. Please record any settings you change on paper or as a note to yourself so that you can put them back.
1) Run a surface scan of the drive. It's possible that one or more files have bad blocks, and they're only being referenced when you first boot up. This can be a LONG test, so plan accordingly. If you have more than one, check C: first, but check them all. Close all software on the machine before starting, then: Start->My Computer, then right click your hard drive (C:, etc.) and choose Properties. Click the Tools panel, then click Check Now. Click the "Scan for and attempt recovery of bad sectors", then click Start.
2) Temporarily set the "Power Scheme" in Start->Control Panel->Power Options to "Home/Office Desk". This should disable hard drive spin downs. I don't think this is the problem, though, since normally the power profile will not spin down the hard drive until it's been idle for many minutes. Not likely during bootup
3) Check Event Viewer for any service failure error messages and try to correct if possible. Start->Control Panel->Administrative Tools->Event Viewer, and check all three categories, but System most closely of all. Sometimes services take a long time to start or fail to start, and this will cause delays that only happen at boot up.
4) On my machine, I found that the "Terminal Services" service was causing long delays at startup, since I log into a domain at work from remote, and when I first log in the domain is not reachable. The Windows Explorer would come up after I logged in, but would quickly become unresponsive for up to a minute, then things would "catch up" and would be fine for the rest of that session. Since I do not use any of its features (i.e. the "Fast User Switching" capability and "Remote Desktop") on my laptop I have disabled that service. Note that if you choose to do this, you lose the aforementioned capabilities, and you also may have trouble installing or deinstalling certain applications, such as Norton/Symantec Antivirus, that strangely need Terminal Services to be running while being installed/removed (but not when regularly used). You can briefly start the service if you run into such problems. If you need these services, ignore this
This thread probably would get more response in the Support forum:http://notebookforums.com/forumdisplay.php?f=80
Hope the problem clears up, it's annoying when the machine does not respond!