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Identical results laser scan after laser scan.

My programs give me identical results for the auto features that are extracted from the COP. The first time the program is ran everything is fine, but when ran again which includes COP empty command and new laser scan to make a new COP I get identical results and my 3 point COP-to-CAD (1000pt, 20 interations refinement included) alignment gets screwed up. The results are identical out to 5 decimal places. If I run the program once, then close program and close PC DMIS 2014.1, then start PC DMIS again and load the program again I get repeatable results that are good and they are not identical. Anybody have a idea whats going on here? Also PC DMIS runs slower and slower as the day progresses. I'm using 2014.1 with a Romer Arm and RS2 laser probe.