Deleted windows partition still in MBR

Hi, I searched google all day long and found out some clues about what could be the problem (even found someone having the same problem as I have) but no solution to repair beside formatting and reinstalling from scratch.
What happened is that I had a Vista partition on my primary HD on my Mac Pro. I bought a new HD to move windows to this new HD so Mac OS can regain some space on its HD. I tried to use Winclone as mentioned on some forum but was not able to boot on the new partition after the restore process. So I did go ahead on deleting the Boot Camp partition on the first HD and reinstall from scratch on the new one. But now, when I use option at boot time to choose my start up device, I see 2 windows disk. One which is the new install, but one that lead to a missing operating system error. I did tried to remove my new HD to see if there would still be a windows option and yes, there is one and it is the missing operating system one.
So for what I understand from reading around the web is that probably, my protected MBR in the EFI partition still has the information about the Boot Camp partition that was once there. So I tried to rewrite this by creating a new Boot Camp partition on the first disk and then deleting it again in case the Boot Camp Utility had not made fully its job the first time, but with no luck. I then tried using rEFIt to sync the GPT and MBR but again, with no luck.
Also, now that I have rEFIt installed, I see 4 windows option at boot time. One legacy OS, 2 windows and one that offer me to boot windows with EFI.
So if someone as any idea, is in front of a similar problem or do know how to update/restore the EFI partition please let me know.
Best,

Hi,
Another little update after a couple of unsuccessful tentative to fix the situation.
I tried to use rEFIt to sync back the MBR from the GPT, but I got this error:
Status: Analysis inconclusive, will not touch this disk.
Error: Not Found returned from gptsync.efi
So, I tried to use Time Machine to restore my main HD after a complete repartitioning/reformat, but even after that I still got the same issue: 2 Windows partition from the start up preference pane in Vista and at boot time after holding the option key and although I only see one Windows partition under the start up preference pane in Mac OS, it tries to boot Windows from an non existing partition and display the missing operating system error.
I am now out of idea and since I don't have time for a clean install, I think I will try to live with it for now. Thanks for all suggestions.

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