How are you resetting the device see this
For Power cycle mode Programming, XRES pin is not required. But the Host programmer must have
the capability to toggle power (Vddd, Vdda, All Vddio’s) to PSoC 5. This may typically require
external interface circuitry to toggle power which will depend on the programming setup. The power
supplies can be brought up in any sequence, however, once stable, VDDA must be greater than or
equal to all other supplies. Have you tried the Jtag programming setup?
Whelp the problem was just the solder connections on the header that the MiniProg3 connects to on the PCB. Everything is good to go now :)