Because of the current status of FGRun's future VS Aircraft Center, I'm not sure this is going to go anywhere but I wanted to put it on record just in case.
I have discovered that the order of the aircraft entries in fg_aircraft on the first tab of FGRun dictates what aircraft is actually chosen during the "Select an Aircraft" phase in the second tab assuming two different versions of the same aircraft and same folder name are used in two or more aircraft repos. I used to be able to select any of the different versions of aircraft. Now only the aircraft folder listed in first priority in the first tab will be selected. I think that even includes the default c172p in fgdata "svn". If you have an additional "fg_aircraft" entry in the first tab and that aircraft folder has a c172p in it, It will be the selected c172p regardless of what you select in the second "Select an Aircraft" phase, even over the default in fgdata.
This make the addition of more than one aircraft repo, worthless.
Is it worth the effort to file a bug report?
This is on a Windows system, I haven't checked Linux.