XRES mode requires that the board is powered prior to starting the program. When MinProg3 is used to program a board in XRES mode, it first checks for the power at the pin connected to the Vtarg pin of theMiniProg. If that pin is not powered, it does not acquire the device.
If you are trying to program CY3280-20xx6 kit using MiniProg3 and external power, even though the device (Vcc) gets powered from the external supply, the Vcc_prog pin at the ISSP header of the board is not powered. Thus, MiniProg3 does not detect power and hence does not acquire the device. In order that the device is programmed, make sure to Vcc_prog pin is connected to the Vcc pin using an external wire.
Note that the MiniProg1 does not do a power detect check and hence tries to program even if the Vdd pin of the MiniProg1 is not powered externally.