I've been pondering updating the navigational data in FSX by using Hervé Sors' Navaids update. For a long time, I've been hesitant, fearing the update would break something in the simulator, but I finally came around and went ahead with the update. Of course, problems seem to arise...

On approach to KJFK (v2), runway 22R, the plane doesn't come straight in on the runway, but askew. Also, when using GSX to jump straight ahead to the runway, the plane lines up too far to the left. I've tested using two different planes (PMDG 737 and QW 787) and they both behave the same way.
It's just as if the ILS, LOC and runway definitions in the KJFK scenery are ignored (despite being on top of the scenery list), and instead the simulator uses the Navaids update.
Any ideas on what to do to remedy this situation? Of course, uninstalling Navaids and reverting back to 10+ years of old definitions is a possibility, albeit not a tempting one...

I haven't had time testing all the other FSDT sceneries I have, so I cannot say if this problem is related to KJFK only.