The way to check the feathering shaft is to remove both blades and turn the bolt/nut that holds the feathering shaft. If the blade holder wobbles, the shaft is bent. If it is a slight bend, then you need to remove the FS and roll it on a flat glass surface and check if it's bent. I get the impression that a bent FS will vibrate and throw the blades out of track.
Another culprit to vibration is a bent Main Shaft. The E-Sky MS is not hardened steel and can bend easily in a small crash.
Those are just my guesses as you indicated you balanced your blades.