I was experiencing the same issue in P3D v.4.5; finally found the issue - seems as though P3D saves some sort of flight file automatically. I had turned on 'auto-save' in FSUIPC thinking that app would automatically save changes to any settings made in FSUIPC automatically. Turns out - P3D was auto-saving the 'flight file' which was causing the annoying stutter. So, the stutter I was experiencing within my hardware setup at least, has been solved!