I just read through this entire thread and wow...nice job keeping the sim community's reputation up guys!
I don't have access to DCS now but I think the assigned altitudes for the waypoints you set in the editor are true altitude (actual feet above DCS sea level) which means that any deviation in temperature will have big impact on what your altimeter reads at a given true altitude.
If I recall it correctly this effect is even evident when using the standard weather which I believe is 15 degrees C, QNH 1013,25HPa etc. I remember I found it frustrating when the tankers wouldn't fly at an altitude which made sense, except when spectating them from F2, there they were maintaining their assigned true altitude.