I don't know how much PCIe bandwith a miner takes up, but i guess the reason could be in the different PCIe data rates the mobo supports.

e.g. my board has one PCIe slot with the full x16 bandwith and an additional one limited to x4.
It could also be the crossfire thing, as the first card has too many mining operations running to properly support the second card with enough data.
Just a guess because i don't know what interface the second card uses to get it's data from...