Glad you got it working eventually. Definitely don't use gparted to change the partition table, because it doesn't seem to be aware of the GPT/MBR hybrid that OS X uses to allow Windows booting. You should've used diskutil instead (if it would even let you make that change). I'm also a bit surprised that setting the boot flag made Windows boot again and didn't prevent OS X from booting (which is what it did in my case), but whatever.

I think your theoretical solution would probably work, but it might not be worth it for you at this point.

Also, it's possible that I did the procedure mentioned in the hint when booted from a different physical disk from the one that had the partition with the msftres flag set. And yeah, I was using Leopard (10.5.1 at the time).