Hey Joey,
I'm having a similar issue within Cleanflight all motors spin at the same speed but when I go through my receiver instead three of the motors are roughly at the same speed and one just shuts off.
I completely agree with finnen, but . . .
The three-running-one-stopped is bad. Your MinThrottle isn't high enough. effectively minThrottle is the minimum "on" signal the ESCs can be sent. When you get into flight, if any one of your ESCs can shut off at minThrottle, then at low but not off throttle, that esc can be commanded to "idle" low enough that the ESC will turn "off" . . . and it takes a little time for an ESC to spin back up to idle . . . as you tumble to the ground.
Go back to your motors tab (props off please), and spin up the motors
one at a time. Find the lowest throttle each motor runs smoothly at (you should now have one number for each motor). If these are within 10-20 points of each other, the calibration is close enough. Your min throttle should be 10-20 points higher than the highest of these numbers.