JAE - Can you give an example problem.
I've found it checks well with ACI code. Even modifies hef and ca1 per D.5.2.3 & D.6.2.4 respectively. Maybe that is where your discrepancy is arising (if your close to 3 of more edges) - I've got no idea without an example, but running though some ACI examples its spot on...
If you give a rough example - I'll check it out (I've used the program quite a bit and understand a few of its quiks fairly well - EX: on LOADS Tab | Load Source - "ACI 318-08" should be Chapter 9 & "ACI 318-08 Appendix D" should be Appendix C - also, if you select "Seismic Design "C" or Higher" it applies the .75 Factor per D.3.3.3 to PhiNn and PhiVn, it is the still engineers responsibility to ensure ductile failure.)