When you set either of the FPS controls in KC, it writes a value into the WoW configuration file.

This value persists, even if you start WoW without using KC.

Your options are...

1. Use the console command mentioned above to uncap it.

2. Edit the config file yourself to remove the cap.

3. Run KC, change the value to something higher, launch WoW, quit KC.

60 FPS is higher dps than 40 fps,
I would put good beer money on that absolutely not being the case, but I understand why you wouldn't want to unnecessarily limit your frame rate when you're not boxing

edit:

4. Use WoWMain instead of WoWAlt when you're not boxing. That's what I do, actually.