A few guesses. Have you looked at the motherboard BIOS version to see if it supports the 1100T? If not then burn a new BIOS, sorry if this is something you have already done.
You might try running the Windows 7 installation program being careful to not touch your existing Windows 7 drive to see if you can run a clean installation of Windows 7.
Had a problem once with using the AHCI configuration option in the BIOS, Windows 7 must be adjusted to use that or it won't boot. Not sure if the converse is true.
Also you might look at your boot drive ordering.
If your windows boot loader isn't getting run or isn't configured right even though we know that it was before, you might try to fix that using something, not sure what program to tell you, I use Norton Ghost for that.
I'm not what you would call a hardware expert but have always seen my way through my problems, wish you luck.
PS: I always go completely through my BIOS settings whenever I get new hardware, has worked for me for 14 years.