I have Minitrack LX3 too. And it works .
There are already two topics on CN:
I try to describe my procedure perhaps you see a difference?
1. Focus dslr on a bright star
2. Level Tripod
3. Mount your camera on the ballhead (When I was doing this after PA, my Rig was moving and PA was sometines gone)
4. Do polar alignment using the supplied polar finder.
5. Turn the clock
6. Do Framing ( You can try to do this before turning the clock, but by turning it your camera moves too)
Take pictures ( I use internal delay Timer or a remote trigger)
Does the clock sounds the same without the camera as with mounted camera?
Be Careful with touching the mount after PA.
Hope this helps?