I found the solution to this problem today. Just as you got no answer here I haven't seen anyone else pinpoint the cause yet. Basically the SSD doesn't have a boot sector so Windows installs it's boot sector to the first available mechanical drive. If you leave the Windows disk in, you'll notice that if you ignore the "press any key to boot from cd" prompt the boot loader on the cd will load Windows from your SSD. The problem is logically when you go to install a new hard drive with a fresh OS you probably went into BIOS and set the SSD as the first bootable hard drive. Windows put the boot loader on the first bootable mechanical drive (the second bootable hard drive) so your pooch was screwed. If you go into BIOS and move the SSD down the boot order by one drive you should be able to boot into Windows normally.
If this helps, please go to the blog post I wrote about this problem at the link below and click on the google ad at the top so I can earn a few cents.
http://suffolk757.com/blog/2010/06/05/fix-kingston-ssd-boot-problems/http://web.archive.org/web/20140417212549/http://suffolk757.com/?p=290
