Windows 7 on 2 system partitions

You said you got the error after two Startup Repairs. But to rewrite the System boot files requires up to 3 full Startup Repairs with reboots no matter what it reports. I just wanted to make sure you'd done this.

If so then your options are to leave F as the boot drive for C, Reinstall with F drive unplugged, or shrink C from the left by 200mb using Partition Wizard Boot CD Resize Partition - Video Help, then create a Primary NTFS partition named System Reserved there and Modify>Set to Active, then run the 3 Startup Repairs.
Partition Wizard Create Partition Video Help
How to Set Active or Inactive with Partition Wizard

Any idea why the system favors this disk over the other? I admit F was set first disk to boot while I was installing Windows on C (the other disk). maybe this is why?

I am going to reinstall, but I want to avoid this problem happening again.

edit: read my edited last post to see what I mean about system repair.

Then unplug all other HD's as should always be done during Win7 install.

Follow these same steps as for Clean Reinstall - Factory OEM Windows 7 to get a perfect reinstall.

As long as you ran 3 Startup Repairs with reboots no matter what errors you got then you can also try to run from repair Command Line the bootrec commands given in Step 7 of Troubleshooting Windows 7 Failure to Boot

I tried bootrec to re-build the BCD using these steps:

• bcdedit /export C:\BCD_Backup
• c:
• cd boot
• attrib bcd -s -h -r
• ren c:\boot\bcd bcd.old
• bootrec /RebuildBcd

I export fine but when typing "cd boot" gives me a cannot find specified path...

It seems like nothing wants to work

Last bump.

Did you try the other bootrec commands:

bootrec /fixboot
bootrec /fixmbr

Sometimes these work when the others don't.

Then if you're about to give up the installation anyway, no need to back up BCD:

bootrec /rebuildbcd

Now try 3 separate Startup Repairs again.