Hollywood, I'm having the same issues with VA not starting DCS BS2 missions using "Mission Start" voice command. I did as you suggested in your message: Changed all ptt buttons via direct setup and changed the "pause" key to the "`~" key in both DCS Options->Controls as well as edited the profile "Mission Start" command to use that key as well.
It's still not working correctly. When I leave VA running after trying the Mission Start command, after about a minute the ptt keys start working again and, among other log entries, the log displays the following with a red radio button:
Command canceled: Another command is not allowing others to execute.
Also, the profile reset command seems hosed as well. Depending on where I am at when issuing a Profile Reset command, it will hang for about a minute then I've seen it display either the same error as Mission Start: (Command canceled: Another command is not allowing others to execute), or errors reading the temporary .lua files (mission.lua and I think options.lua)
I don't know if it makes a difference in my case but I do have DCS installed on my mechanical drive D: while Voice Attack/Vaicom is installed on my ssd drive C: