Herman, when I click the add-on checkbox, I get a message "Add-on airport file not yet located. Do you wish to locate it? If you didn't get that message, then you must have checked the Airports menu item "Look for Add-On Airports in Scenery Library" - in which case AIFP would already have known where to find the add-on airport. The Traffic Analyser Airport menu has several functions related to the specification of add-on airports. Their purpose is described in Section 11.1 of the user manual.
AIFP searches the active Scenery Library items looking for a .airport .bgl file for the designated airport. It does not expect to find more than 1, so stops the search immediately upon finding the first. By naming the main airport .bgl "ZZZZZ" in this case, you ensured that AIFP would not find that file if there was another airport .bgl in the scenery folder. Because this is such an unusual situation and the time it takes to analyse every .bgl contained in every active scenery folder (resulting in "dead time" from the point of view of the user), I am reluctant to search the entire library every time. What I may be able to do (since Jon apparently has enabled this capability in ADE), is ensure the "found" add-on contains parking.
In the meantime, if you name your main airport .bgl, or alternately, name your additional airport files, such that the main file will be analysed first (standard files sequencing is observed), I think you'll find the Traffic Analyser will perform normally.
Don