I believe both boxes will remember what was checked the last time you completed that action. I do not have SW in front of me this second but try changing it and see what happens when you run it a second time.
It doesn't or at least mine does not, I wish they stop changing things around, I keep accidently thinking I am doing a save as instead of a save as copy and modifying the wrong parts. I want the old way back!
uncheck the box next to "____ is being referenced by other open documents. "Save As" will replac..."
Open an assembly
Open on of the components in the assembly
This will reset SWX for you
Jason, thanks for this tip. We finally upgraded to SW2013 a couple weeks ago and I had been screwing things up all over because I was used to the "save as copy" check box being unchecked. Huge sigh of relief after following your instructions and having the default back to unchecked. It's the little things...