Hey just catching up on your post. Nolapete is right, your cure time wasn't long enough. I read where you said you "Jumped the gun." I think that was the problem. My success with silicone, pond coat, and other liquid rubber brands involved letting the silicone around the glass cure for a full week. I haven't had any issues with liquid rubber adhereing to glass and up over the silicone, as long as you let the everything cure well. I think this is your problem. Cure time for the liquid rubber ranged from a week to 14 days to fully cure. I'd be willing to bet that the cure time wasn't long enough either for the silicone OR most likely you filled the tank too soon with water and the rubber could not set up fully (the water neutralized the unfinished cure). But mostly likely I'd bet it all revolves around the cure time.
Is your work shop heated? I know that the cure time depends heavy on the temperture and humidity. I think 50F is the minimum temp for curing liquid rubber and requires around 2 weeks to fully cure. I've even timed tank builds for spring and fall builds because I'd have to apply coatings, epoxies, etc in an unheated-no a/c garage. Curing time for epoxies and liquid rubber in August himidity in the midwest is hell.
On another note, it is possible there could be the issue of the spacers you used between the glass and the wood. I'm not for certain because I have never used spacers before, but silicone squishing out was never a concern. Perhaps the silicone needed the extra crush factor that the spacers prevented.
1 more scenario haha, bare with me here, perhaps there was an issue with the wood surface that the glass is glued to, with regard to not being square, flush, plump, etc. Typically the silicone, which works as a gasket, will fix minor discrepancies, imperfections, flaws such as an unlevel surface. The problem again, could be the spacers, interfering with the silicone's ability to "fill the flaw" or gap, what-not.
(I grew up in an auto-repair shop, this was a constant problem with intake manifold gaskets. The front/back gasket worked more of a spacer, than a gasket. Once installed and engine running, the pressure would always build and blow out the front/back gasket. This was all because the front/back gasket worked as a spacer and took that much sealing power away from the silicone used to seal it. The solution? Throw away the spacers and just use silicone. This worked 100% of the time IF you let the silcione fully CURE! haha)
Ok I think the only scenario I didn't present is global warming. But serious, the cure time, Nolapete hit it on it and I 2nd it.