Mike,
If the joints are out that much (1.5mm) then I would look to see if the rails are joined properly. Sometimes you can get one rail sitting on top of the joiner, instead of in it. With Code 100, 1.5mm is about half the height of the rail - you don't want to be filing that away.
If the rails are joined properly, your difference could be caused by a few other things: different code rail, like Code 83 and Code 100 meeting. I have done this a number of times, as it is difficult to see the difference sometimes. Also if the track is the same code, but from different manufacturers, the ties (sleepers) might be different thicknesses, causing the rail to come out at different heights. The solution to both these is to shim the lower track up to meet the higher track.
Hope that helps.
Andrew