UPDATE: I figured out the issue. The loaded application was locking the main thread. I booted it into safe mode then re-flashed it with another app and it works fine now.
I am having some strange issues with my Photon. It boots as normal, launches the flashed application just fine but it shows the Photon as offline. If I hold the setup button it won’t go into setup mode. I put it in DFU mode and then upgraded it to 0.4.4rc1 and went through the CLI setup. It says it’s online but as soon as I try and flash it from build.particle.io it never turns magenta and just says offline.
The boot LED order is normal going from flashing green to normal pulsing blue/green.