Ah. Now we get to the heart of the matter.
You can have your third-party program run a command like this:
"C:\Program Files\Microsoft Office\OFFICE11\msaccess.exe"
"C:\MyAppFolder\MyApp.mdb" (that's all one line)
This will open your Access application, which would automatically run your
AutoExec macro.
However, as you say, you have different types of uploads. Given sufficient
information to differentiate between them, Access will be able detemine the
correct upload type for each one.
This raises this question: can you identify what type of upload is needed
based on the name, extension, or location of the downloaded file?
If Yes, then you could easily make a form that opens automatically when you
start your application (forget the macro). Have that form do these things
automatically when it opens:
A. Look for the downloaded file.
B. Based on some factor above, determine the type of upload needed.
C. When finished, close the application.
This could all be done in Visual Basic in the form's code module. Post some
more specifics on the file names/extensions/locations, etc. and the upload
method(s), and we can get you some help on accomplishing it in VBA.