I think Gillie's right, you have some diagonal braces at the front but none at the back, so I suspect you have a lot of bending going on at the rear where the side supports meet the top. The aft support/top joints aren't nearly as stiff as they are at the front. A 90 degree joint isn't very stiff, so diagonal braces between the vertical and horizontal tubing at the aft top corners would stiffen it a lot. Gel coat is very brittle, so I suspect you would have already seen cracks in the coaming/side deck radius if your problem was too much deflection in the glass.
I'd be careful about adding braces or gussets under the gunnels, because if you create local hard spots in an otherwise soft panel, you'll get stress concentrations at the edge of the hard spots and CREATE cracks that you might not get otherwise! It sounds like you've already got fairly robust pads under the mounts, so I would suggest surrounding those pads with something like 3/4" balsa core wrapped around under the gunnels and tapered at the edges, and then put several layers of 1708 over the whole works to create a cored panel that will be very stiff. And I'd use epoxy resin for maximum bond strength and flexibility.
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