Did you run Rebuild MBR from PW Disk before trying Startup Repair again? I'm just asking.
It is hard to say what caused the Repair to finally work. Was the installation detected earlier to repair? Did you note what was reported in the Repair details?
Since we are dealing with the boot sector here, I thought it might be important to resize Windows 7 back over it. This was only a hunch and may or may not have had an effect. Sometimes resizing Windows 7 over the boot sector requires Repairs so we know it can matter. If the installation only showed up to repair after that then it likely contributed.
Here are troubleshooting steps
you can use to monitor your System resources for problems, check logs for repeat errors to resolve, generate a System Health Report, test hardware if ever indicated, etc.
I would also immediately scan your system with Belarc Advisor to audit the installed Product Keys including that of Windows 7, in case you need to reinstall. After determining if Windows 7 is running fine, also save a backup image which can reimage your HD in 20 minutes if Windows 7 ever becomes irreparable. Backup Complete Computer - Create an Image Backup
You can mark the thread solved at top.