On the PSoC5 CY8C5888LTI-LP097, there are pins marked UART on 12_6 and 12_7. When I configured these to be regular digital input pins down pull-down resistors, one pin was permanently HIGH and one was permanently LOW.
I have a UART in my project, but it's TX only and I connected it to 1_7, not 12_6.
I didn't read anything in the app notes about UART pins. I'm using the pins marked I2C and they work fine.
I solved my problem. The KitProg programmer that is connected to my CY8C5888LTI-LP097 had an active UART. I removed the zero-ohm resistors that connected them.