Hi, if the bubbles are on top or near the top, this may help. I was looking at pictures of your molds and noticed that you don't have any sprue holes. I used to cast plaster with rubber molds. I'd put sprue holes in the mold so that when casting, the top side would have extra room for the bubbles to escape. Below is a simple example.
http://www.micromark.com/part_mold.html
The stuff that I was doing was relatively small. I'd use a 60cc syringe and lancet needle to inject the plaster. If, after trial and error casting, I saw bubbles forming where there was no sprue hole, I'd stick a lancet needle into the mold flush with the interior of the mold to act as a sprue.
I've tried to cut and burn holes through the rtv rubber without luck but the needles punch straight through it. I bought the hypodermics and needles at a farm store that catered to dairy and horse farmers.
Best of luck.