The stratum difficulty could be higher on the 2 card system resulting in fewer shares per minute. Check your stats on your pool if they allow that.
All three cards are on the same machine and connecting tot he same pool. The weird thing is that when the miners first start the share count goes in favor of the pair, but after a while they start to even out.
that's pretty normal, like Timgt said, check your accepted hashrate on the pool, as long as it's consistent it wouldn't be a problem. Just means you get fewer high difficulty shares less often than the low difficulty shares. Many pools adjusts difficulty based on your hashrate (vardiff) and that's most likely what you are seeing as the share count goes.