voltage/polarity issues with isoclean transformer

I need a bit a help here. I have had 2 PT-3030G II Isoclean isolation transformers for some time. I am in the process of re-wiring my ac distribution. Since I am building some new power cords to and from the Isoclean transformers, I pulled out a voltage tester to confirm polarity and voltage. (I never did this before on the Isocleans). I am getting reversed polarity and "off" voltage readings from the entering side of the transformers to the exit side. Neutral and line voltage are reversed and the exit voltages are not where they should be in many cases. Has anyone tested their isolaton transformers voltage and polarity? Do isolation transformers reverse polarity? Of posible further interest, I found some interesting readings coming out of the Isoclean 80A and 50A distribution boxes as well. I have not contacted Isoclean but will. Any thoughts? Thanks