When I go to make a replacement across a project and select the "prompt on replace" option, the "Search results" window annoyingly pops up on each replacement and must be closed to go to the next replacement.

Am I missing something?

Thanks, I'm on 5524 but it's been this way for quite some time.

I'm not sure I got your right.
First you select "prompt on replace" and then post this message that the "prompt on replace" is annoying you.
If you don't select this option and click Replace All button, would this satisfy you any better?