I previously had a Windows 8 and Ubuntu 12.04 dual boot on my SSD in my desktop. Before that I had a Windows 7 and Ubuntu dual boot on my HDD. The only BIOS setting I changed was I put my SATA controller in AHCI mode from IDE in order to support booting from my SSD. I had some issues with support for programs I needed in Windows 8 so I decided to re-install windows 7.
The problem that occurred was after installation; my computer would tell me it couldn't find an operating system. I tried installing again multiple times, clearing both internal drives, trying different combinations, and using boot-repair under an Ubuntu live CD to fix the MBR, nothing worked and it would occasionally tell me Windows could not install to the drive I had selected. Now I manged to install Ubuntu by itself on a partition of my SSD.
Now when I tried to install Windows 7 SP1 in the other partition, it simply wasn't recognized and Ubuntu would just boot up instead. Using boot-repair to reinstall grub fixed the recognition issue, but when I booted Windows to complete the setup it told me "Windows Setup could not configure Windows on this computer’s hardware" and the setup just failed. Each time I try to boot into Windows again it tells me I need to re-install.
I've never had these problems before and I don't understand why Windows 7 refuses to work now.