If you swap the riser cards does it only recognize B (which was A) or not boot at all? I wouldn't see why it would make a difference if A was in B or visa versa. This may narrow down if its a bad risercard.*
OR*
take the RAM out of riser card A and put it into riser card B and see what happens.*
Not really familiar with how the new riser cards work but I'm thinking that maybe one fo the sticks of RAM went bad so its not being recognized at all possibly even making the riser card not appear. RAM can go bad at any time. Doesn't matter whether you paid $50 for it, or $50,000 for it.*
Basically do a lot of swapping out and switching around, but MAKE SURE you know what was working and what wasn't working. So keep a way of remember what RAM was in riser card A. You know for sure that the RAM in riser card A works. This way you won't accidentally be putting bad RAM into A and then wonder why the computer won't boot at all anymore.*