Holy crap dude, that thing should be in the ghetto DIY thread. Part of your problem could be the nuts only engaging your pane dividers by a sliver of metal. The other part could be that silicone is not great for sealing to acrylic, unless it's just forming a gasket (you're using it to seal around the bolts, and hold pressure that way.)
Taking the bolts out one by one and resealing MAY help, but probably not because new silicone doesn't stick well to old silicone. If you want to "do it right" take that whole front panel off and throw it in the garbage. Make a new one with a wide enough center pane divider, and reinstall your windows with NEW bolts, using a modern adhesive like DOW 732 or that 3M marine adhesive that actually sticks to acrylic and stainless steel, instead of regular pure silicone.
what kind of bolts are those?