This is due to the fact that even if you might not notice it, your click becomes a double click, because sometimes we don't press the button firmly enough. So the first click opens the menu, and the second one opens the first item on it, which is "open new terminal", even if you don't get to see the menu because it's too fast.
You could try to adjust the variable multiClickTime to, lets say, 800 milliseconds:
echo "*multiClickTime: 800" >> $HOME/.Xresources
This basically ignores any click unless it's been at least 800 milliseconds since the last one (almost a second). You can lower the value if you think is too long.
Hope it helps.