Ok, your popup will go away when you drop the fs_game_base argument. It's not appropriate anymore for the standalone folder setup (it only has its purpose in D3-style folder structures).
So, change your shortcut and only set fs_game=fms/missionname, omit fs_game_base.
Sweet that fixed it, sorry for getting to look at what turned out to be an end user issue. Just one question though, I have short cuts for SVN and TDM, so how that I have removed fs_game_base, I assume there is now way in the shortcut to swap between different game installs..? or could it be -
TDM - fs_game=fms/mission
SVN = fs_game=svn/fms/mission
Just tried that and get the pop-up again.
Edited by Bikerdude, 25 April 2018 - 03:56 AM.