Trobuleshooting Boot Issues

I have a Pixhawk from the beta batch, it has performed well no issues until I tried to connect an IMX6 to it.
Then the here lights went out, never could get the imx6 to pair to the controller but that is a different topic.
When I went to reboot the Pixhawk after removing the IMX6 and putting standard rc control back it hung solid orange on the cube base LED front.
When I hooked it to the usb port on my surface to MP it kept alerting high voltage on usb port and the orange front and rear LEDS would rapid flash and periodically turn off and on.

I took it to a desktop, and was able to get it to boot, and even upload the latest firmware. I thought OK I am back in business
But when I hook it back to power and only power via the brick and 4s, it will not boot.
Is it possible the cube is still hosed?
Or is the carrier board or power module most likely bad.