Yep, it's a pain in the ass. I too use left shift for crouching but had also some problems to configure it. If I remember right, it conflicted with the helicopter key settings in the config file despite the fact that you can't change them in-game. I think I deleted the entry "left shift" in the config file and was then able to reassign left shift in-game.

Nice to see this topic reposted. I hope it gets included in 2.2. Of course only to improve realism and immersion, not to make me hit finaly these pesky little tanks