It should be able to boot at least.  

Power cables are plugged into both cards right?
If the 9800GT boots by itself, and you are getting rid of it, why do you need to make sure it boots with the radeon?


You have a bootable CD, like a WindowsPE disc or UbuntuLive disc?  See if that works.  Could be a power issue.  It might be 500watts, which should be enough to boot at least, but could be an amp issue maybe?  Does the PSU have different rails, and each GPU on a different rail?



Suggestions might seem silly, but sometimes something obvious could and can usually be overlooked.