Importing model from Altium creates slight deviations in tolerances (.00001 or less)

I am working on an integrated electromechanical system and when attempting to mount boards modeled in Altium by my EE contractor, I have found that the angular relations are very, very slightly off. I am talking about 89.9995˚ instead of 90˚. This is a huge issue because it makes it nearly impossible to create mates as Solidworks finds a solution with the parts hundreds of meters apart. The only workaround I know of is creating my own planes in the models I receive and mating using those. Is there anything that one of us is doing wrong, or just some small check that will fix this?