I did have the same issues with the V5 print set window and did report them (in the olden days of the newsgroup)
The problem never seemed to be addressed for a very long time and I kind of resigned and got used to dealing with it, until a couple of updates ago it finally got resolved.
Unfortunately I really don’t know what fixed this problem for me and can’t track down the exact point in time/upgrade that made the problem finally disappear.
But as this behavior continues on your side I suspect it might be related to a specific hardware or software (plug-ins, mouse drivers etc) configuration?
While snapping can interfere with the placement of the set print window, the problem described by Steve1 is another:
Any movement of one of the corner points would make the set print window “jump” resulting in a complete offset (usually – in my case – to the right and down placing the set print window partially outside the screen)
As I said, for me the problem vanished a couple of upgrades ago.
P.S.: I just experienced the “jumping” behavior, no black lines etc when printing pdf’s
Edit: by “just” I meant “only”.