I didn't have this problem at release when I played through it but recently wanted to give it another go with the current version and custom levels, which I successfully installed without Steam workshop (instructions can be found here).

Now I got the big problem that the right click is sometimes working and sometimes not. I often have to click 5-7 times right to pick something up since it doesn't always register it. This is effectively breaking the game since you have to work fast.

I have already deactivated game-pad support in the menu and unplugged my directInput pad just to be sure but it didn't change anything.

Any ideas what might be causing this and how to fix it?