So Umberto, it's not because there's nothing visible that could affect the rwy headings or magnetic variation that it's...
I can only confirm that nothing at PHNL can affect the Magnetic variation.
In fact, after installing PHNL everything was fine. But after I added other sceneries (then PHNL was not anymore on the top of the scenery library) I had wrong rwy headings
That's more evidence it's not caused by PHNL.
The fact that happened with the Tropical sim scenery and it was caused by a .BGL in that scenery, doesn't mean that PHNL could cause this as well. That scenery probably added or modified some navaids, and navaids includes the magvar in their parameters so, a wrong magvar parameter in a navaid redefinition might disrupt the magvar readings in the sim.
This is not the case at PHNL, that doesn't change or add any navaids, there are no navaids anywhere in the scenery (if you open the AFCAD with an editor, it will show navaids coming from the *default* scenery).
The fact that you have to put PHNL on top every time, might simply means the problem is caused by another scenery and, by putting PHNL on top of it, the problem introduced by the other scenery is overwritten by PHNL, that is taking priority over it. In this case, PHNL it's *fixing* the issue, not causing it...