I have almost the same problem, but I can't fix it this way.
I had windows 7 x64 installed on C: and then I bought a new disk and installed windows XP 32bit on E:. Of course I couldn't boot win 7, so I repaired the installation with boot cd. I then installed and run EasyBCD 2. I can choose which windows I want to boot now, but XP gives me an error about not finding NTLDR. I tryed copying NTLDR and that another *.com file I can't remember the name of from win XP cd, but it didn't help.
Another thing I noticed is my drive letters are different in windows 7 than in command prompt of win XP repair thing. And also in EasyCD if I look at the summary, it says I have win 7 on C: and also win XP on C:. I suspect boot.ini has wrong information, but can't find a way to edit that file.
I appreciate any help, thanks!