I think you need to read the manuals again in regard to material angles. See the section for CQUAD4 elements in the NE/Nastrain Reference Manual and the section for defining material angles in the FEMAP Commands manual. When you define a material angle in FEMAP you are not rotating any coordinate systems, rather you define a vector direction or coordinate system axis which is then projected onto each element and the material angle for each element is then calculated. This angle defines (for each element) a local coordinate system for stress/strain output. NASTRAN actually has the capability of defining material angles by reference to the x-asix of a coordinate system (MCID field on the CQUAD4 or PSHELL cards), but FEMAP for some stupid reason won't output the MCID values; FEMAP calculates the material angles and outputs the angles for each element on the CQUAD4 cards. To turn on results output in the material coordinate systems you set the ELEMRSLTCORD parameter to MATERIAL in the NE Editor. Unforturately I have never found a way to figure out in FEMAP what coordinate system the stresses and strains are in once they are read back into FEMAP. (Another problem with black box postprocessors). There is a way to transform stress output from element to a material coordinate system inside FEMAP, although again there is no dianostics provided by FEMAP to tell you what it is doing. The transformed stresses are put into new output vectors.
Without knowing detailed specifics of the coordinate systems, element orientation and desired material angles it is impossible to diagnose your issue. I suggest that you build a very small, simple flat plate model in the y-z plane, apply a simple axial load, define a material coordiante system that is rotated at 45 degrees in the y-z plane, and run the model 3 times getting stresses in the basic, element and material directions. If you do this and still can't understand the results then post a description of your results and we will take it from there.