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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.

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That error message is also caused by this bug, however it has suppository been fixed in SP1 so I doubt this applies to your case. – Annan Nov 27 '12 at 11:05

Windows has to live on the first primary partition. Use your favorite partitioning tool (cfdisk, for example) to make a primary partition for windows. Install windows. Then make a second partition and put grub (or the whole ubuntu root) on it. When you install grub, make sure you install/write to hd0 (or similar) and not hd0,0 because if you install the grub-mbr on the first partition (windows) then you will erase the windows boot loader.

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Are you sure windows 7 must be installed onto the first primary partition? I've heard otherwise, "More recent Windows operating systems (Windows 7, XP, etc.) can be located on any partition" - wiki – Annan Nov 27 '12 at 11:01
    
More recent Windows (...) can be located on any partition, <b>but the boot files (bootmgr, ntldr, etc.) must be on a primary partition.</b> You could maybe work something out with a (shared) /boot formatted with fat32, or even have two boot partitions. Practically though, this may turn out to be a cumbersome task. Perhaps it's easier than I think with "recent Windows". The solution I offered is the <i>simplest</i> way to get things working. I chose the easy way which is to not fight windows and let it occupy the first primary partition. This may (not) be suitable for you. – Ярослав Рахматуллин Nov 27 '12 at 14:14

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