It was the stand alone version that I installed. I had the anti virus turned off as you suggested. Now the following aircraft have no landing gear and have nothing functioning - Level D, PMDG, Quality Wings, CLS (probably some others since I didn't test any more).
But that doesn't depend in any way from the Addon Manager or Couatl, regardless of their version. As I've said, if an old version is loaded for any reason, the only products that might be affected are our own.
If those airplanes requires their own modules on the DLL.XML or EXE.XML files, if something happened to those files, their own modules might not being loaded.
It's possible that either you have corrupted the XML files trying to fixing the problem manually (our installers, including the QW one, can't corrupt any XML files, because they use the standard, official, Microsoft XML parsing routines to modify them). Or, it's possible that you run another installer in the meantime, which has issues with parsing standard XML files in the correct way as XML and wrongly parse them as text files, the PMDG is known to have this issue for example.
To minimize this risk, we even run a specific official W3C utility, that clean the XML and make it formatted perfectly, so even less robust installers that runs after our own will never be confused, but if it has somehow failed to run (antivirus, maybe, but it would really a buggy antivirus the one that would block the official W3C formatting tool...), it might be possible that *another* installer that you ran after our own, failed to parse the XML file correctly (this is a fault of the *other* installer) and corrupted it.
And of course, our installers also make a safety backup of your XML files as they were before running them so, in case something fails (like the computer crashing in the middle of an install), it should be possible to retrieve them. They are named dll_xml_before_addon_manager and exe_xml_before_addon_manager and are located in the same folder as the normal XML files, which is %APPDATA%\Microsoft\FSX