IIRC you get the best performance when you put the biggest DIMMs into socket 1 and 2 of each riser card. In your case, swap the 1GB modules from riser A, socket 3 and 4 with the 512MB modules in riser B, socket 1 and 2.
I have a question similar to this one. sorry to jack.
I have just installed 2 gb of ram into my early 2008 mac pro.
The new ram was not recognised in slot 2. But work in Slot 3.
So now i have 1gb x 2 in slot 1. and 1 gb x 2 in slot 3.
Will this effect speed in anyway if they are not placed in sequentially?
The weird thing is . when i tried the new ram on its own in slots 1. one of the sticks shown a red light. but now they are both working in slot 3. Is this a common thing? is it worth me trying them again in slot 2?