Has anyone got this problem? In what way is the gog version different from the steam one that it makes it incompatible?
Trade rank cant be increased, the pirates are acting weird, and the phanon corp is bankrupt
The steam version does not have this

I feel this is something you should contact GOG support or Egosoft about so they can fix it.

I was able to run LU on X3AP v3.2D. I never upgraded to 3.4 for fear that it would break LU. Maybe roll back to that version and see if it helps. If that doesn't work, maybe try using the NoSteam.exe similar to the Steam setup.