You bet, the deeper it is in the tank, the more pressure it'll take to get the bubbles out. I ran into kinda the same problem - changed batches, and it quit working (Hagen ladder mounted with the outlet about sixteen inches under water). The danged gas/water interface (meniscus) in the tube hung right at the water's surface - move the tube, and the meniscus followed. I found out that the Tee I was using to connect the two 2-liter bottles together was a bit small for the tubing I have, and it was leaking slowly. Replaced the Tee, gave the bottles a good shake, and it's been cranking out 35+ bpm since. Check your connections - if everything is tight, give your yeast reactor vessel (isn't that an impressive phrase?) a bit of a shake to wake things up. It was tough finding the leak in my system - I did it by sniffing all the connections!