Occassional Disk Read Error at Boot

I've been having this same issue for about 6 months honestly, and I fear that it is slowly damaging my computer or Windows installation's integrity.

Here's how it goes:
I very, very rarely am able to shut down my computer. When I shut down my computer for more than 6 hours (it seems any less than 6 hours, this issue does not occur), I get the following error on boot:
A disk read error has occured.
Press Ctrl+Alt+Delete to restart your computer.

It doesn't do this after a reboot. It only does this after a long period of being shut down.

From there on, I just have to keep hard booting my computer, and eventually it will kick into gear and start successfully. Sometimes, it takes longer than normal to start successfully, maybe 6 hard boots, sometimes just 2. Sometimes it will boot past the Windows screen and then just remain idle forever. Then when I hard boot, I am told that Windows has failed to start and there may be an installation error. I can continue to hard boot again and it will start successfully.

I've tried literally everything: defragged, defragged the page file, checking the disk for errors, CCleaner, checking memory diagnostics, running Windows startup repair, blowing out my case, etc. Any ideas?
I'm on Vista x86 Home Basic.

Welcome back to the Forum,

Heres my take on the problem. First back up all of your stuff ,as it may be that a hard drive failure is imminent. I hope not, but lets play it safe.
Take this hard drive test and lets find out for sure, but first back up
Test Hard Drive HD Diagnostic or this test Hard Drive Diagnostics Tools and Utilities (Storage) - TACKtech Corp.

Do you hear any strange ticking sounds? If yes, it is most certainly hard drive.

If you pass the hard drive test, the worst is over. It will just take a diagnosis to figure out the cause.

http://support.microsoft.com/kb/929135
Try in clean boot and see if the problem persists

To test the integrity of the system, you can try and SF command.
http://www.vistax64.com/tutorials/66978-system-files-sfc-command.html
If errors are found run three times.

In addition, take the Windows 7 upgrade test. If you have certain hardware issues it will be detected with this test
Run the upgrade advisor to help discover hardware problems
www.microsoft.com/Windows/windows-7/get/upgrade-advisor.aspx

Here is some information about Hard Drive problems and testing
Hard Drive Testing Tools - Top 7 Free Hard Drive Testing Tools - Hard Drive Diagnostics