I've built several Tri's with both APM and Pixhawk. I've found that's kind of normal, actually. Have you flown it yet? In flight, the autopilot takes over to correct yaw and where the servo centers in a static situation doesn't really matter.
With APM, the tail rotor servo can be off to one side and it doesn't go to center until you arm.
With Pixhawk it centers as soon as you press the safety button before the motors are started.
With neither controller will the tail servo respond to stick input until it is armed. Sitting on the bench with the props off and motors idling, yaw full right, return the stick to center and the motor will be off to the left a little. Yaw full left, return stick to center and the motor will be off the right a little bit.
Take the props off, arm it and throttle it up. Holding the aircraft in your hands, yaw it back and forth and observe the operation of the tail rotor servo to see if responds to changes in yaw. If it does it's working normally. I don't think it happened from 3.3.1 to 3.3.4. Because my APM Tri with 3.2.1 does the same thing.
If you take off and it wants to yaw one direction or the other, you can set the trim with the MOT_YAW_SV_TRIM param. But in any flight mode using the compass for heading, even that shouldn't matter as long as the yaw P is set aggressive enough.