Not saying this is the case, but an update doesn't necessarily mean that it fixes a bug. It could restore a default that was changed accidentally. Unfortunately I haven't experienced a situation like you describe so I can't say how to get out of it.
I think the key is to find out what in Sonar can link clips in some way so they react as you describe...maybe there's some option or check box somewhere...then if it happens again, you'll know what to do. Anyone?