Meaning, if you right click and make a custom startup line for ARMA2, those launch options are for ARMA2. The problem is the start up line is loaded for each instance of the game separately. Then select 'Set Launch Options' which opens the launch options input window and allows you to enter your custom launch parameter, like what is shown in Fig 1 below. While in your library of installed games, right click on the game title and select properties. There are several ways to load mods, one popular STEAM method is the startup line parameter change. The menu dissapears because essentially the menu is a hybrid menu from ARMA2 and OA. The problem is if you launch Combined Operations, you lose the mods manager and the ability to load mods such as ACE2 and others from the menu. This is ARMA2 OA's new in game mod manager which works very well with the retail version of the game but is gimped in the STEAM version. When one loads OA you are greeted with a very nice menu choice called 'Expansions'.
I have walked several of you through these procedures and felt that a SPARTA post would be beneficial to the community as well as my limited reserve of sanity. I've heard a lot of discussions in TS3 regarding loading mods with a STEAM installed ARMA2 and ARMA2 OA and there seems to be a lot of confusion regarding STEAM, ARMA2, ARMA2 OA and ARMA2 OA CO.