Deleting Vista's boot sector

I hooked up a 2nd hard drive to my computer and did a clean install of vista on it. After everything is done, I noticed this problem: When I do a shut down and turn the computer back on, every other time it would hang and not boot into Vista. In between it would boot into Vista like it should. After much researching, I came to the conclusion that I need to remove the boot sector on the original drive?

The original drive's first partition has been formatted in Vista, the 2nd partition is the partition containing the factory's Recovery Image. Is there a safeway that I can delete the boot sector of this drive so my computer will boot properly everytime? Thanks.

 

Try Making the Current Partition Active or Set the Drive as Primary bro

 

It already is. Everything runs fine right now except for every other cold boot. Is there a way I can delete the boot sector from the original drive (which doesn't have Vista anymore except for the Recovery Partition). I think the problem is that Vista sees 2 Vista Partition and will alternately boots each hard drive. There's a way to clean the hard drive and return the drive to it's "Virgin" state, which I think will fix the problem. But I want to be able to keep the Recovery Partition so I need a way to do it in Vista some how.