Thanks Dana. I went through the AN and did not find any reason for failure, however one of the techs did find the problem. They had put this 5 volt part into a 3 volt system! I am accessing it remotely, and also did not have the latest schematic so I did not realize what they had done. It turns out that Cypress has a compatible 3 volt part so we have it on order. I seem to recall that some of the GPIO lines are compatible with 5 volt inputs, so it might have worked of they had just supplied 5 volts to the part, but a 3 volt part is a better solution.
Thanks again, Russ
Yes, you can do level shift with the Vddio quadrant settings, but
constrained to <= Vdda.
http://www.cypress.com/documentation/application-notes/an72382-using-psoc-3-and-psoc-5lp-gpio-pins AN72382 - Using PSoC® 3 and PSoC 5LP GPIO Pins
SIO pins one exception, they are 5 V tolerant.