I bought the software by yesterday. It installed without any problems on non Standard place. I have multible instances of FSX running on the same machione and some housekeeping for the appdata, roaming etc.
files. Reason for this is software development.
In addiotion my installations are on a Win 7 German 64bit OS, FS is German and Spanish ACC, so additional Problems.
Problem was:  Loader was directed to the wrong FS.
OK: there is a Flight 1 registry tool and a Batch that should correct the reg entry:
hkey local machine\Software\Microsoft\Microsoft games\\Flight Simulator\10.0 mit SetupPath regSZ <your path>

That one is not used by the loader on a 64 bit system

instead you need to use:
hkey local machine\Software\WOW6432Node\Microsoft\Microsoft games\\Flight Simulator\10.0

I know at least some other software that also reacts like that and does only read the WOW6432Node entry.

Hope that helped anybody.