As far as I know the MiniProg3 will connect via SWD interface onloy to a PSoC3. Can you alter that setup or does your board permit that? Or are you using a development kit?
Miniprog3 *B Revision Update:
Cypress Semiconductor has completed a hardware update to the Miniprog3 to address hardware issues seen with programming, ESD, and power management. The Miniprog3 revision, either *A or *B, is indicated using sticker on the back of the programmer. The following are a list of updates made to the Miniprog3 *B programmer.
Updated Hardware to Improve Power Cycle Programming:
The Miniprog3 hardware has been updated to better improve power cycle programming for all PSoC devices. It was discovered that the Miniprog3 *A programmer revision did not correctly implement the power cycle programming methodology. Due to this issue the Miniprog3 *A programmer could not correctly support power cycle programming for PSoC 3, PSoC 4 and PSoC 5LP devices. This specifically impacts customers who do not route out the XRES line to the programming connector or disable the optional XRES line on certain devices. The *B revision of the Miniprog3 will support power cycle programming for all PSoC 3, PSoC 4 and PSoC 5LP devices.