Some premium motherboards like MSI BB Marshal can absorb massive electric loads without affecting the stability of addons on the mobo.
The downside is that those boards cost a lot ($400 or more) due to having high quality components, capacitors, chokes etc.
Yes, a low quality board can limit the overclocking capability of a card if a lot of power is being drawn through too many slots (75W for each card), at some point the power draw will choke and some cards might be getting sub-par power.
One way to circumvent this is using modded extender cables w/ Molex which feed the card the 75W from the PSU rather than the motherboard.
but if I plop a second card in, at best I can get 1000/350 on one and about 930/350 on the second.
Try OC'ing them individually. If the problem persists then those are the hard limits of the cards you have, i.e they can't be pushed higher.
I have some 5850's that wont go even a bit above 880mhz, and some will go easily past 1ghz.