It's normal this won't be fixed by reinstalling the airports, since the problem are not the airports themselves. When you have misaligned AIs, the problem is never the airport itself, but a conflicting scenery from another scenery or product you have installed.
The most common culprits of misaligned AI, are AFCAD made for AI Traffic Packages like MyTraffic, TrafficX, etc., which are supposed to "enhance" a default airport, but it should be removed if you use an addon airport.
You can use the GSX customize parking position option to check which is the AFCAD being in use, so you will know what file you must delete. Or, you can use the free FSX Airport Scanner utility to search for conflicting airports and remove them.