Does this mean the Accuracy of the different models is different? I know this causes problems in the manufacturing module. If so, it's a matter of opening the offending part/assembly and clicking
File -> Prepare -> Model Properties
You'll see a line for "Accuracy". I think you want to make this vaue the same for all the involved files. I've learned over the past few years to set these to "Absolute" with a value of 1.0e-05 in inches.