Have the same issue here. Getting kicked by BattlEye for using "AutoHotKey". Spent half an hour in Waterfront, no problem. Switched to Social for 30 seconds, kicked.
I did have AutoHotKey installed, but it didn't complain when I played Heroes and Generals (which also uses BattlEye) with it installed. Other than a test script I put together once, I never used it, so I'm not sure why it was kicking me for a program that wasn't even running.
I've now removed any and all files of AHK, including cleaning up the registry (the only things left are the .txt registry backups). However, it still kicks me. Sometimes it doesn't even kick me at all, or it kicks me after a while.