These are generic solutions, maybe will work for you:
1-Try registry tools:
FSX TWEAKFS REGISTRY UTILITY V1.21
Flight1 FSX/FS9 Registry Repair Tool, http://www.flight1.com/view.asp?page=library
This should assign the proper register paths to FSX-SE
2- If this not works, you can create a "fake FSX" in the FSX boxed default installation: C:\Program Files (x86)\Microsoft Games\Flight Simulator X
You need to put in the Flight Simulator X folder the FSX.exe (not need of the executable, create a file in worpad and save as fsx.exe).
I don't know how of FSDS works. Depending of the use of FSDS, maybe you'll need to copy folders from the FSX SE to the "fake FSX" to work with them and then return to FSX SE.