In PC click Control Panel.Programs/Uninstall and you see FSDT KJFKV2 installed together with other installed programs. I thought you might have known that.
That's where it's supposed to be. But it wasn't clear, from your previous message, if with "Programs", you were referring to:
1) the "C:\Program Files" folder OR
OR
2) the "Programs" group that can be reachable from the Windows Start Button
OR
3) The "Add/Remove Programs" section of the Windows Control Panel, which list what programs can be Uninstalled.
That's why I had to ask, because in the case #1, there might be a registry problem, if it was really installed under C:\Program Files, but your FSX was installed into C:\FSX
Addon Manager states Product installed and active.
Ok, now it's better. You initially said it's says just "Active", and were missing the most important part of the sentence, which is the indication if it's installed or not in the Scenery Library, which is of course very important to know, in case you don't see the scenery, that's why I had to ask for a clarification.
Now that you indicated the correct sentence, it seems the installation has been correct and the scenery is found where it's supposed to be.
This is stated although Product has not yet been paid for because the buy window is not highlighted for that purpose.
Again, if the Addon Manager says the product is Active, it means you HAVE purchased it, no questions about it so, it's fairly obvious that, if you already purchase it and activate it on this system, the program wouldn't allow you to mistakenly purchase it again. If you wanted to buy another copy for any reason, you can always do that from the Website.
If you believe you never purchased JFK V2, the possible reasons why you are seeing it indicated as "Active" are:
1) You HAVE purchased it, but you forgot about it
OR
2) You haven't purchased it, but you activated it using a Serial Number from someone that has, like a friend...
OR
3) You are confusing JFK V1 with JFK V2, so you had JFK V1 active on this system, and it's still active, but you are trying to use JFK V2...
I do not know why you say there may be conflict as this is the only FSDT airport installed with no runway markings of any description as stated. KJFK V2 is the only airport within the FSDT Folder in FSX.
But of course the conflict is NOT caused by "another FSDT scenery", or "another FSDT scenery in the FSDT folder". If there's a conflict, it's always caused by an entirely unrelated scenery which can be everywhere.
As discussed many times already on the forum, whenever you suspect there might be something "default" or not right with a scenery, the cause is almost always a duplicate AFCAD from another product, even not a scenery. The worse offenders are AFCADs coming with AI Traffic Package like Traffic 360, My Traffic, Traffic X, etc.
You can use the free "FSX Airport Scanner" utility to search for file duplicates at any airport.
But again, are you confirming here that the ONLY problem is the missing runway markings ? Do you mean everything else is working normally ?