I have windows 8, so there is no start menu, I do not see a separate launcher at all for secret missions 2 within the wing commander folder on my hard drive. I have uninstalled and reinstalled still nothing. I have played secret missions 1 fine through my wing commander shortcut on my desktop. Any help would be appreciated.

Just wanted to let everyone know this issue has been resolved. Opened up notepad, clicked file then open, selected all files, went to the c drive/wc/dosboxWC_single , you then see this

@ECHO OFF
mount C "..\WC"
c:
cls
loadfix -1 wc
exit

changed the wc to sm2, saved and closed everything double clicked on the wing commander 1 shortcut to start the game and it starts secret missions 2

You shouldn't have to do that. GoG installer is supposed to install a SM2 link into your start menu program files directory.

Look inside GoG folder and go I to wc1&2 folder and then look in wc1 folder.

Try reinstalling. It should look like this.

The first shortcut is SM2. SM1 is in the menu in the main game.

I seem to have problems also launching Secret Missions 2, but I can launch it in DOSbox on Win 7-64 just fine, after the title scree however it freezes at a window with the text "Enter 5", which I'm assuming is the piracy check, I just installed this a few days ago as well and I can't seem to find this issue anywhere on the forum. Any help would be appreciated

It's not actually frozen. I think you just need to type in random number, and then hit enter..

I have no idea what that 'enter 5'... it doesn't seem to serve any purpose. Maybe your right that its leftover for copy protection?