I actually found the problem.
First off, the wires coming off my cc3d, I needed to release the signal wire from the connector and move it all the way to the end into pin #8.
Now go to LibrePilot, configuration tab, hardware, and make sure the cc3d is set to PPM_PIN8+OneShot
Now check the Output tab and set 1 (1-3) & 2(4) to PWMSync. 3(5,7-8) & 4(6,9-10) will be PWM.
Once all that was set I had no problems!
I hope this gets you up and running.
Curious...are you also setting up a Eachine 250 racer?
If so I highly recommend doing the VTX relocation mod. I put mine on the bottom plate in the back and moved the battery to the top plate. It's not so ass heavy now and the poor TX antenna doesn't take the full brunt of roll over crashes.