@Nick2K4
My suggestion is to get one of those hacks on Aminet that make the drive stop clicking.....then that flickering will stop, since you said it stops when you insert a floppy?
Also if you use your Amiga on a TV like I do, I suggest getting Visual Prefs, Magic Menu, and Tools Daemon.
Visual Prefs thickens the Border lines and you can change bright white lines to light grey ones and black lines to dark grey. This will seriously reduce flickering on a TV. Also use a genlock that has S-Video OUT. It looks just as good as a 1084s.......actually better in some cases.