I've seen this complaint many times. I've yet to see a response from SolidWorks. SW is apparently unwilling or incapable of fixing it's auto-reversing mates problem (almost always involving a concentric mate, which other software don't have problems with, by the way), where if you allow it to reverse a mate on its own, it pretty well destroys your assembly. Their fix was to give you a pop-up offering to do it. That really doesn't help anything. You wind up being pestered to do things no one wants done. It might as well ask if you want to receive dog feces in the mail, again and again and again. Is there some reason that there's not an option to say "No, I don't want to SW to automatically change my alignments, not now, not ever, please leave me alone". There are a number of nuisance alerts like that I'd really like to get rid of, actually.