..or the hole was made too large and the plexi large to accommodate.

As regards the caulk, you must get both surfaces VERY clean of silicone. Caulk remover, scrubby pads on a mandrel which can be bought at the paint department, elbow grease. Not even silicone likes to stick to silicone.

I just ordered two tubes of Cow Corning 795 structural silicone for my modified DDW sliding main hatch. I have used it with great success repeatedly and over time in reinstalling windows and such. About 8 bucks a tube and amazingly, Amazon has it. Or you can find it at an industrial supply house.