Does anyone know a work-around for this "known issue"? If a user is trying to save a document (e.g. Invoice), the extension is showing as .NL if the user has Adobe Professional installed on their local machine (i'm guessing some browser plugin comes with it)

are they trying to download the generated PDF from transaction?

yes

I turn off the user preference to download the file - and let it open in a tab - and then have the user print it to PDF as opposed to hitting save or download

something wrong with your user's file association, by default when print button is clicked generated document is always pdf. You can force force the download to pdf only via user preference. Tell the user to set their preference for download to PDF. Home>Set preference.

That's the preference I normally find myself un-checking when this happens.