Files are not the same. Any harm in making the files the same by simply copy one to the other location?
Difficult to say: you might have some sceneries that were installed in one cfg and other in the other one so, what you should do, is probably lots of merging, which can be tricky.
Is there a preferred way to run FS9, explicitly as an Administrator or not?
I think your issue might have been created by the fact that you sometimes ran FS9 as Administrator, sometimes not, and updated the Scenery Library in both modes so, the two scenery.cfg got out of synch.
It's usually best not to run FS9 as Administrator. What you should do, instead, under Vista or Win7, is to INSTALL it in a different location than the default C:\Program Files ( or C:\Program Files (x86) under 64 bit os ).
The issue is: lots of problems with addons are because the C:\Program Files folders is not user-writable so, many 3rd party addons fails because they try to write in that folder, because it *was* possible to write there, under XP, where those products were originally designed.
But, if you install it in a different folder ( I've always install FS9 into C:\FS2004 and FSX into C:\FSX ), everything will work, without running as Administrator, even older XP-only products, because that folder was created by YOU when you ran the FS9 or FSX installer so, you own it and you have full read/write permissions, even if you are not running as Administrator.
