I should also mention that in my %PROGRAMDATA%\Virtuali\Couatl folder there is both a folder called fsx and fsxse. Will this cause an issue?
That's how it's supposed to be: there's a separate cache for FSX and FSX:SE. That's why I told you to remove the *whole* folder, so it would remove both caches, regardless which sim they belong to.
I tried your suggestion and the folder fsxse was recreated and the fsx folder wasn't.
Assuming you removed the whole folder (the Coautl folder, which contains both caches), if only the fsxse cache has been regenerated, it's because you are running FSX:SE in a Dual installation mode, because you had FSX installed.
Unfortunately this didn't fix the problem but when I created a copy of the folder and renamed it fsx, everything works now.
That's because you probably removed FSX *AFTER* you installed FSX:SE. This will cause issues, so it's best to reinstall FSX:SE *after* having removed FSX, so it will setup itself to run in "Single" mode.
Also, with the UK2000 scenery, when loading up the sim, the aircraft is sometimes loaded just a bit off of the actual gate parking spot. I'm not sure if this is all related though.
If with "loaded", you mean you go to a parking using standard "Go to Airport" FSX menu, it means the AFCAD position is not precise, and this is totally unrelated to GSX.