Update-3 is which PSoC Creator? Could you show us its exact version number?
I used kitprog to program PSoC4000S without any problems, not sure PSoC4100S plus. I will try at my side.
Have you removed other connections on your kit?
How about this project? Does work or not? I have programmed the external device with using the bridge on the kit. Could you double-check hardware switches on the board, or you can try other debug/programming tools?
I had the same problem until I've read the release notes from the PSoC 4100S Plus Kit.
You have to use at least the KitProg 2! The programmer on the CY8CKit-042 uses the KitProg 1.
I don't know if the PSoC MiniProg 3 can also flash the new device family.