Most annoying problem you're having there. Mine's working v.well (when it's not scarring the poo out of me!)
Speaking for myself I've never seen the point - remove the whole upper half: More room, fewer cut fingers.
Like you to me it sounds like 'ringing' of the analogue signal somewhere along the cables...
...If my Indi's ribbon is causing no issues to me & your VGA cable has given no trouble in the past I wonder if it's possible you're just 'plain unlucky' & you've got a combination of lengths that is promoting the reflecting of signals - cable length = exact multiple of signal wave-length or some-such...
...maybe a different length VGA cable will do it..?
I suppose you could try wrapping the ribbon-cable with a grounded sheath or put one of those 'ferrite doughnuts round it if it does prove to be interference.
What resolution(s) is your Amiga running & what kind of monitor are you using?
Could it be your monitor is making a hash of scaling the Amiga's output..?
For instance, if you have a TFT does the situation improve if you use a screen mode nearer the native aspect-ratio of said TFT?