Photon setup flashing cyan with a "quick red burst" (now orange burst) [Solved]

I see you’ve got the Photon soldered to a custom PCB, so chances are that the external circuitry does overstress the USB power supply on connection attempt causing the key hanshake to fail or your PCB design does cause degraded antenna performance.

Try a different cable (these old Spark USB cables weren’t too good), a 2A minimum USB power supply and possibly a uFL antenna (needs to be selected in code too).
How does your keepout area around the chip antenna look?

There was another thread by @UMD having troubles with a mounted Photon and reception a while back
Photon SoftAP mode - mobile cannot obtain address

and also this
Photon SMD Antena, keepout zones, and ground loops