I've uploaded Moksha packages that no long screws with randr settings at startup to the unstable branch - hoping to include this in 3.2.1 bug fix release early next week. Seems to work as expected on my intel system. Will try it on my nvidia setup here shortly.
Anyone who updates to this and does a reboot or two with different dual screens let me know if you see any issues. This should hopefully resolve the "black screen after disconnecting external screen and then starting up later" bug a few people have had.