HI Carlioian,
I have followed the switch to FSX-SE also. I had to clean the registry before installing FSX-SE, and every other appearence that had something to do with the old FSX-MS environment. Indeed, Steam works better in frame rates and is most certainly more stable. Installation of my add-ons worked fine as long as I downloaded the most recent versions.
When installing the EFB (new install, I thought) I ran into the same kind of problems. I did not log what I did, so I can't mention all the details. But for sure I cleaned out every appearance of the EFB software, files, directories, registry, the works on both, the PC and the client (my notebook). After that I just installed the EFB on both machines and that went like a charm. No problems whatsoever.
New Navigraph install (had to change the directories of course) and the datamanager did it's job like it should.
So my rough guess is, that you have some cleaning to do to get the EFB working.
Good luck,
Dirk