IF you installed the OS from the DVD.
AND you didn't change ANYTHING,
I can't see any way windows could have affected the system unless
it reflashed your BIOS. I don't think it did that.
I'm too lazy to reread the thread, so some of this may be redundant...
Did you unplug the hard drive and see if it would boot from DVD?
Did you swap the DVD to the primary port?
I have seen situations where the system would skip the DVD
and boot directly from the HD. But if I removed the HD, it would
boot from the DVD. I'm just guessing that my DVD drive was marginal.
With no other available boot options, it may try more times before
giving up.
There's a thing called PLOP boot manager.
I've used it on older systems where the bios didn't let me boot
the way I wanted. I booted PLOP from a floppy
and used it to select the boot device.
http://www.plop.at/en/bootmanagerdl.html