EDIT: Thank you SO MUCH for your help. Now everything works just fine! Thanks for your patience!
I was quite sure of it.
We suspect the messed registry might be due by either a defective installer, or by someone out there suggesting to just copy the FSX registry into the FSX:SE one, in order to force installers that only recognize the standard FSX, to install into FSX:SE, without taking into account how FSX:SE really works (side-by-side with FSX mode or stand-alone mode), since this seems to affect lots of users, and it's confusing our installers, which PROPERLY supports both modes of operations...