While trying to use the alternate SWD pins of the PSoC 5LP kit- the USBIOs which can also be used for programming, we saw an unusual behaviour. We were able to program the IC at 3.3V but not 5V. We used miniprog connections only, but simply wired the alternate SWD lines instead of the standard one. (For this, we used a USB mini-b cable, cut it, took thbe wires out and connnected it to the USBFS jumper and the wires to the miniprog :) ).
As mentioned, we were unable to program at 5V operation. but if we soldered R30 (i.e. shorted the Vdda and Vddd pins) the programming worked. It is some ramp up issue of the analog regulator of Vdda. It ramps up slower than Vddd and thus miniprog remains unable to acquire the port.
I hope this info helps everyone.