This should't happen: couatl.exe is a full windows 32 bit executable so, it shouldn't trigger the 16 bit Ms-Dos sub-system.
Something that might have cause this, is the executable has been corrupted on your hard drive, which can also explain why the program crashes. If this is the case, you can fix it very easily, by simply reinstalling any scenery that comes with it (all of them) OR, by installing the Stand-Alone Addon Manager. It doesn't make any difference which method you'll use, because both will get the current version of couatl.exe from the internet in any case.