its installed alongside fsx boxed. but i uninstalled the boxed version after installing the steam edition, and the registry is correct (HKEY_CURRENT_USER\Software\Microsoft\Microsoft Games\Flight Simulator - Steam Edition\10.0)
No, it's NOT!
Normally, when FSX:SE is installed stand-alone without FSX, the correct registry key for it, is HKEY_CURRENT_USER\Software\Microsoft\Microsoft Games\Flight Simulator X\10.0, the same used by FSX.
But if you uninstall FSX *after* you install the Steam edition, the FSX uninstaller won't obviously "fix" your FSX:SE keys, because it doesn't know anything about them. A correct course of action would be Uninstalling and Reinstalling the Steam edition too, so the registry keys would all be like FSX, which is how FSX:SE is when installed on a clean system.
Note that,
you could have proceeded with the installation, if you simply replied NO to the 1st request to install into FSX Steam mode, because the installer is smart enough to check the FSX folder then, and check if there's a Steam FSX installed there, so you still have a chance to install into Steam in "Single mode", even after your replied NO to a Steam "Dual Mode" install.
This was already discussed here too:
http://www.fsdreamteam.com/forum/index.php/topic,11322.msg89158.html#msg89158