I'm also confused on how you siliconed. Silicon should not leak so you didn't get the spot that's leaking. If you do silicon a piece of glass over the hole, I'd say it's better to do it on the outside, the pressure ect will be better. Actually silicon doesn't bond to acrylic does it? I don't know. Does your bulkhead have that tape stuff plumbers use around threads? On glass tanks if you tighten the bulkhead too much you can cause the tank to crack. Just things to be wary of. Sorry I couldn't help that much.