I doubt you have counterfeit parts. I noticed the different logos some time ago. I have various Cypress CY8CKITs with parts with both logos and my FreeSOC2 board has a different logo than yours.
I think you are into hardware debug mode.
Can you try doing the swap test by changing the chip with the PCB and check whether it works.
It looks like your board is hand-built. Based on the fine-pitch of the pins, it is a bit easy to have a hidden solder short or a cold-solder joint.
Sometimes my tech colleagues hand-building a PCB needs to use a focused heat gun to quick reheat the CPU pins to reflow solder to minimize bridges or melt cold-solder joints.
We figured out the problem. the VDDA pin was tied to a 3.3v supply instead of 5v.
From the datasheet:
VDDA must be the highest voltage present on the
device. All other supply pins must be less than or equal to
It programmed just fine, but there is another problem we are seeing that doesn't make much sense, but I'll make a new post later if we can't work it out.