Realizing this reply is out of date, I had the same issue; Win 7 64 bit with sudden onset of very slow boot ups to the point boot up was failing altogether but intermittently. It could take 20 minutes to achieve a "stable" boot up and even then any input lagged dramatically. I read some ideas such as editing regedit to alter HKEY_LOCAL_MACHINE\SYSTEM...
To make a long story short, my c-drive is a WD 1002... 1TB. I had about 360GB on it and had tried radical defrag to no avail, although it seemed to work once. After I got the computer to finally reboot after five unsuccessful attempts, I started moving a lot of stuff off it onto another drive just to save it, winding up with only 100 GB worth of programs and non-data file stuff.
I then did the defrag and optimized the residual files using Ausilogics, and I made an image back up using Macrium Reflect. Previous attempts to save the drive using Macrium Reflect, crawled along at 1-4 MB/s. This time, it went at >650 Mb/s and took only about 30 minutes to complete. My previous attempts wend on for hours and then failed.
I didn't use the regedit option. Just removed a lot of files and then defraged and optimized the rest and it is now booting up and running just like new. In the mean time, I have bought another WD 1002, figuring that was the problem, but I guess I'll just keep it as a back up as everything is working great as is.
Anyway, that's my story. Hope it helps someone. Sounds a lot like a similar problem.
PS - chkdsk found no issues. nonetheless the drive started acting flaky and then got worse over a period of two days with attempted backups running at 1-3 Mb/s and then terminating and repeated failures to boot windows at all. Now, with the above, everything is 100% back to normal. I still suspect there could be a problem with the drive, however, and am glad I now have a brand new back up just in case -- and a recent image that is running fine. I just hate it when I have to reinstall Windows and re-load every frickin' program from scratch.