I'd imagine that (as it was released way before bootcamp) the OS X DVD would not be aware that it is using the two partition maps.
When I tried something similar, (triple-booting OS X, Windows and Linux) I used a tool called rEFIt to make sure everything played nice together; it replaces the default bootloader (the thing which decides which OS to load) and can sync the partition maps, plus do a few other tricks.
Can be found at:
http://refit.sourceforge.net/
I'd make sure you have everything well backed up, then see if rEFIt can work it's magic and make everything work right. If you image your drive, if it does all go wrong you can just blank the disk and restore it to how it was from the images..