Okay, THAT's why. 640x480 and other super small resolutions are ridiculously unstable and a nightmare for hud making. I've never even done anything with 640x480, so bear with me.
You're probably best off messing around with more values inside flagstatus. Go for lesser increments than -50 because that probably moves it off your tiny tiny screen.
I've never done anything positioning wise with the control points so I don't know at all what controls them. Maybe look it up in Doodle's Guide?
Not sure what you mean in the last part.