When there's good contact with all components cooling must be okay. I only can think of two things.

1) Contact at some point is good, but after you install the card contact is lost in some places. Try setting your motherboard horizontally (if it isn't) to see if temps change.

2) There might be something wrong with the water flow. Have your checked the temp of the problem card when running on it's own without the other card connected in the loop?