Elantriell, Are you using Poser 5 or Poser 4/Pro Pack? MAT Pose Edit v3.0.0 doesn't convert bump strength and highlight size correctly for P5 MATs. So if you're using P5 it's possible that the highlight size is way too high. We've managed to solve these problems with ronstuff (thank you Ron!) but there are still a couple of other tasks to do before I'm going to release the update. Make also sure you have all the 8 eye materials in the MAT file (see the screenshot).

Karen,
MPE would support P5 partial MATs if they worked in Poser 5. Poser 5 needs the complete shadertree in the MAT files, otherwise it just uses default values for the properties, thus erasing all the previous values. Only P4 formatted partial MATs can work in Poser 5, but then other problems may rise. So there's really no perfect solution to this unless CL decides to fix this in the next SR, which I doubt.