OSDL announces Patent Commons Project

You could certainly have a patent, and then grant use to anyone as long as the entire program is an "open source software program (as defined by OSI) or Free Software program (as defined by FSF)". A BSD program that used the patented idea would still be a BSD program, and could be widely shared... but it couldn't become proprietary in software patent countries. Yes, this would in essence cause that program to behave legally like a GPL'ed program in those countries where software patents are legal and a patent covers the work, as you noted.

But this is no different than what happens now with patents. If you release a BSD program, and I patent something your program uses, then you can't release the BSD program AT ALL unless I grant you rights (or you fight an expensive legal battle). A patent can turn BSD code into ILLEGAL code, not just GPL'ed code. At least if the patent is opened to "open source software programs", you can release and use the code under some conditions.

Oh, and I didn't make a mistake at the beginning of the sentence; someone can easily patent your ideas AFTER you release them, because someone competent in software is unlikely to want to work at the patent office. It's not hard to patent someone else's idea after you hear about it, then sue them, and the courts mistakenly assume that a patent must be valid because it was granted. It'll cost you millions to fight the patent; are you likely to win?

You really can't help but have all sorts of weird situations like this, as long as software patents are permitted at all. The problem is that BSD is a copyright license, not a patent license; you can't grant the use of a third party's patent without their permission. And notice that this only occurs where software patents are permitted; since they're illegal in most countries, the BSD would still hold sway in those countries.

Patents may have the side-effect of eliminating the MIT and BSD licenses long term in software patent granting countries. In a world were the proprietary people are patenting the wheel, and the open source software developers (the majority of whom support the GPL) counter-patent all they can but only for "open source software" projects, it may not be possible to write code that doesn't step on either set of minefields.