After some testing it looks like it is the laser beam from the Abyss Octopus entity that is destroying the energy door. My guess is that the beams damage doesn't account for a neutral target that it shouldn't be doing damage to. This issue doesn't seem like it would come up or effect anything in vanilla Aquaria. I think the best way to fix this is to simply remove those entities so that they don't have that opportunity. Surprised and glad no one else seemed to have this problem initially after release.
Gary must not enjoy living. Ever after I had to patch him so he couldn't die from energy form he finds a way (sigh). This should be an easy fix but I have yet to find a solution... keep on chugging Mr Bear.