Unable to upload firmware or connect to MAVLink. FMU B/E Blinking rapidly, but blue IO ACT LED is still on.

Howdy,

So I've been unable to upload firmware to my pixhawk for a while now. I tried many things, but I always seem to return to this problem. When I attempt to make and upload my code from Eclipse it ends up detecting my pixhawk and says:
All done!
Skipping invalid documentation tag: 'default'
make[2]: Entering directory `/c/px4/Firmware/Build/px4fmu-v2_default.build'
Loaded firmware for 9,0, size: 879944 bytes, waiting for the bootloader...
If the board does not respond within 1-2 seconds, unplug and re-plug the USB connector.
attempting reboot on COM4...
if the board does not respond, unplug and re-plug the USB connector.
At which point it gets stuck there forever. Any clues on this? Prior to uploading the code, when my pixhawk is powered the main LED is a solid red which indicates a problem, but I do not know how to figure out the problem. I am currently waiting on my buzzer and I'll look at the boot log on the SD card shortly.
I am also able to connect to the pixhawk using the NSH CLI in Mission planner, but when I connect when all of the commands appear it jitters rapidly up and down, instead of having its original smooth auto scroll when outputting data. I don't know if this means anything.
Any ideas?
Thanks for the help!

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I've had no luck uploading new firmware lately using mission planner.
I use apm planner 2 and works just fine to upload 3.2.1

Well, I'nm trying to upload my new code using the software eclipse. I tried uploading firmware using Mission planner before and I was able to select my firmware, but it could not connect to the MAVlink so it could not finish uploading.

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