Josh,

Without seeing the print or the part, I would ask the following
questions:
1) When changing alignments from the plane to the cylinder are you accidently changing your rotation? Remember that you have AI and AR to deal with. I have found that the order of the features used to create perpendicularity can give different answers because of AI and AR
2) Assuming some similarity
with U-Soft, are you using the same reference length as George has suggested?

Just out of curiosity...George sees a hole, I see a protrusion...Which is it?

Good Luck!