I am having the exact problem indicated in the subject line. I'm running DOSBox on a MacBook (13-inch, Late 2009) with Snow Leopard (10.6.7). I've tested this with two different games, so I'm assuming it's a DOSBox issue.

If I unbind the alt key I still can't click when I'm holding it down, whereas if I bind another key to alt, I can use that key to alt-click. So I have a work-around, but it's still annoying.

I suppose it might have to do with the fact that OS X uses alt-click for special functions in the Finder and other programs. OTOH, OS X also interprets ctrl-click as right-click, but that doesn't seem to prevent DOSBox from handling ctrl-click correctly.

update: I was messing around a little more and I also noticed that DOSBox has the same problem with the command (a.k.a. meta) key.