I have the same problem with the Bachmann Empire Builder Set and Atlas code 55 track.  Used the NMRA standards gauage to check the wheel spacing and found that all the wheels were too close together.  I suspect Bachmann complies with a British standard rather than the NMRA.
Bachmann prints a disclaimer on the box that says "Use of non-compatible systems may result in unsatisfactory performance".
By the way, I checked all the measurements on the Atlas track and turnouts and they were all exactly what they should be.