If the object is returned for the all_objects query, then it should be displayed in the folder.
To obtain some more diagnostic information, can you modify the shortcut and add the DebugSQL parameter? For example:
"C:\Program Files\PLSQL Developer 12\plsqldev.exe" DebugSQL
Reproduce the problem (open the folder with these objects) and send me the debug.txt file that is generated in the %APPDATA%\PLSQL Developer 12 directory (e.g. C:\Users\\AppData\Roaming\PLSQL Developer 12).