Identical milled lobes, 180* apart different dimension

Hopefully some bright swiss "guy" can help me with this problem. On my Citizen M32, I am machining a part on front spindle that has two identical lobes 180* apart on the face of part, using the same tools for both sides of part, two 1/4" C. E/M's, one is ball nose, and I am running the same subs to machine and then profile the tips of the lobes. The material is 1.0" pre-heat-treated tool steel. The problem I can't seem to get past is that the same lobe on 25% of the parts that I machined, was .001 smaller (in Z) than the other one.

Like I said I am using a Citizen, with PartMaker CadCam programming, so that is a huge variance! (not to mention out of tolerance)

What are you using For a Guide Bushing... ??...Is it a Factory Housing..??, Or posibly something Pneumatic...???
Can you post the Prg &/or a print, so we can a better Idea of Exactly what your trying to do...
If the prg's the same for both, I would start by looking into your work holding...Could the material possibly be slipping in the collet, hows the Guide bushing tension..are you doing anything on the O.D. of the bar stock that could cause a burr, and in turn give you Z repeatability problems...and of course there could always be a problem with the machine it self, but then you would probably be having more then just this one problem..

Also what are you using for Milling Spindles...Check for play in the Bearings...

Along with what JMS4287 said, look into the index direction when positioning the part. reversing directions can result in slight changes. If they are not the same directions add an index or two to make that happen.
M18C0
G0C90.
C180.