Yes. I should point out though, that at the time of fitting, I did not have the 5.25" bay installed due to some modifications I was making to the plate. I'll have to try again sometime with the bay reinstalled, but I don't see any obvious reason why a Founders edition card wouldn't fit properly.
-edit-
I'll try it out tomorrow and report back to see if it still fits as it should, but in the meantime, can you maybe take some pictures of your problem area?