I think Leopard is probably the key to getting the msftres flag fixed. The rEFIt tool is what let me sync the GPT/MBR tables again, and I think it's also what lets me boot either OS with the 'boot' flag set.

Isn't diskutils the program that comes with OSX? From what I've read, if you try to make any changes to partitions with that, it destroys all the data on the disk, which is what gparted avoids. If I had known about rEFIt's GPT/MBR sync utility before I clicked the 'boot' checkbox in gparted the first time, I think everything would have been fine and my NTFS partition would have remained set to "Microsoft Basic Data" or whatever Bootcamp originally set it to that lets OSX work see the partition correctly.

As of 10.4.6, diskutil will let you resize journaled HFS+ volumes without erasing any data, assuming the structure of the disk and the data allow it. I'm not sure if volumes with any other filesystems can be resized, though, so I'm not sure if you could have used it in this case.