I mostly configure when the FSLabs is loaded, however this issue is new and has worked perfectly before I think your last update.
As I've said, nothing on our recent update can possibly have any effect on this, since we haven't changed anything related to mouse handling, or even the editor, since many months.
What is your frame rate in the editor ? In general, it's always best NOT to use a 3rd party aircraft heavy on frame rate, because the mouse is read at the fps rate ( it cannot be any different, of course ) so, the lower your fps, the less precise the mouse click detection might be.
There's no reason whatsoever to use a certain airplane model to customize a parking, just because you think you'll use that model in regular use. The way GSX works, makes entirely irrelevant which airplane use when customizing so, as long as you use a *similar* model ( like a default A321 ), for the only reason to give YOU some visual reference, it will be fine, and with an higher fps, the whole editor will also be much faster and easier to use, because even movement with keys and rotations are tied to the frame rate.
Whem we do our GSX customizations, we always use the default A321 from FSX on most gates, the default 747 on heavy gates, and the default CRJ for small/regional gates. This way, the fps is much higher ( usually in the 50-60s ), and the editor is way easier and faster.