The location of the mouse isn't going directly over the start button then. Try moving your screen.
I positioned these in the top right corner of a 23" monitor displaying at 1920x1080 so you may have to adjust them a little bit. That's why I included the undetected coordinate grabber.
You can just re-position the screen to match up with it
OR
If you want, just run the coords tool, hover over your start button in game, and hit "Z"
then record the two sets of numbers (eg 246,858) and right click the bot script, select edit script.
On the window that pops up, look for This line:
MouseClick("left",###,###, 1) ; Clicks START to launch mission
and replace the first two numbers (###,###, 1) with your coordinates you just gathered.
Do the same action for the replay button, and you're good to go.

Now just go up top to the menu, and go to Tools -> Compile and select where you want the compiled bot to go to.
Gl, and feel free to ask if you have anymore questions.
Also, please make sure that you're running the game in the specifed resolution correlating with the bot, and that it's in windowed mode, not windowed fullscreen, or fullscreen. Just windowed.