Did you disable the debugging interface for your bootloader and bootloadable project? Imho this could interfere with bootloading. What pins on your target is the miniprog3 connected to when bootloading and what pins when you program the bootloader?
Tried disabling the debugging interface and got the same result, although I believe I did have problems with it while I was initially putting these together so I'll leave it off.
For programming the bootloader, I'm using the SWD pins, XRES, SCLK, SDAT, and GND. It's powered externally but VTARG is connected to our Vcc so the MiniProg can see the voltage. When bootloading, I'm only connected thru GND, SDA (12), and SCL(12). There are 3k pull ups on the I2C bus, and a few other devices, but this same layout was just fine a few weeks ago so I doubt bus impedance is affecting anything.
I would suggest you to get in contact with Cypress directly:
At top of this page select "Design Support -> Create a Support Case" and describe your problem. Leave a link to this thread, so they can see what you've tried alrady.