Hexacopter Motor PWM Imbalance

I have a hexacopter drone and have conducted two tests using different firmware versions: ArduCopter v4.5.2 and ArduCopter v4.3.7.
In both tests, I’ve encountered the same issue:
Motors 1, 3, and 6 are spinning at higher PWM values, while motors 2, 4, and 5 are spinning at lower PWM values.

The snapshots for respective tests have been attached below:
Arducoptor v4.5.2

Arducoptor v4.3.7

I have thoroughly checked the motor alignments and performed multiple calibrations to ensure everything is correct. As a newcomer to ArduPilot, I’m uncertain whether this behavior is expected or if all motors should be spinning at the same PWM.

For your reference, I have attached the drive links to both the flight logs.

Any suggestions or guidance on this issue would be greatly appreciated. Thank you!

You will have to check again as it’s the most likely cause of a Yaw bias.
What is the Lua Script doing?

Hi Dave,
The Lua script is to operate a robotic arm mounted to the drone.
The design of this arm is detachable, so the arm was not mounted during the tests.

As per your suggestion, I’ll check the motor alignments again.

I have checked the motor alignments using a spirit gauge; the motors haven’t been touched since last flight. Attaching snapshots for the same.
Ground Level:

Motor M1:

Motor M2:

Motor M3:

Motor M4:

Motor M5:

Motor M6:

Is there a possibility that I have set some parameters wrong?

Check yaw trim in RC transmitter and on the FC the receiver trim param

The drone seems to experience an auto-clockwise yaw. 1,3,6 CW.
You have a few GPS issues, I am not sure if that is the cause.
As @amilcarlucas said, has your channel 4 yaw stick got a trim accidentally set?

1553 04:35.2 MSG 10091338 ArduCopter V4.5.2 (291be848)
1565 04:35.2 MSG 10091467 GPS 1: specified as DroneCAN1-125
1613 04:35.4 MSG 10209928 GPS 1: error changed (0x00000BE8/0x000003E8)
2989 04:37.6 MSG 12410096 GPS 1: error changed (0x000003E8/0x000003C8)
3534 04:38.4 MSG 13216745 GPS 1: error changed (0x000003C8/0x00000388)
4084 04:39.2 MSG 14014854 GPS 1: error changed (0x00000388/0x00000308)
4491 04:39.8 MSG 14614289 GPS 1: error changed (0x00000308/0x00000208)
17843 04:59.4 MSG 34207437 GPS 1: error changed (0x00000208/0x00000008)
18393 05:00.2 MSG 35008018 GPS 1: error changed (0x00000008/0x00000000)
40412 05:32.1 MSG 66964634 PreArm: GPS 1: not healthy