OK I checked the source code for presenting P3D v2 as an option in the Version Selector. ADE checks for versions
each time it starts. It checks whether it can find a registry entry. It first checks
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Lockheed Martin\Prepar3D v2
It looks for the subkey
SetupPath
If it finds that key and the subkey for SetupPath is not empty then it will display the version in the selector. Otherwise it tries:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Lockheed Martin\Prepar3D v2 again it looks for SetupPath
If it finds SetupPath in either of these then it will show the Version in the Version Selector. If it does not find these keys or subkeys then it will not show the version in the Version Selector.
ADE searches for FS9, FSX, P3D, P3D v2, P3D v3, and P3D v4. It will list each one that it can find a registry entry (they are different for each version but the process is the same) in the Version Selector. When it does this it will show the last used version in the drop down window. It stores the last used version in Global.ini. It
does not store the results of the version checks it makes. It does these fresh each time since it makes no assumptions in advance as to what versions are present on the users computer.
If it finds only one then it will open directly with that version and the version selector will not show. If it finds none then it shows a red version selector.
All the above happens before any reference is made to the settings files in individual version folders - until ADE starts for a particular version it has no idea which settings file and folder set to use.
I have just run a test to see whether ADE behaves properly when it only has one entry (that is start without going through the Version Selector) which it does. I also checked in case P3D v3 could somehow display as P3D v2 in the version selector. I could not make that happen.
There is a way to manually force ADE to display all versions in the list whether present in the registry or not. This is an all or nothing hack and is not relevant since you show only FSX and P3D v2 in you list.
Please check the registry to see if one or other of those entries above are in fact in your registry? If not then I am stumped.