Post pics. Easier to see what you mean. I'll try to give and an answer, but it's a conjecture.
Are you talking about 2 over flow tubes (standpipes)? I'm guessing with no pic, that you mean this.
http://gmacreef.com/herbie-overflow-reef-tank-plumbing-method-basics/
It sounds like both tubes are taking water (thus level) and neither is under full siphon (thus taking air.)
My understanding is that when you have 2 overflows, 1 is supposed to be set lower than the other, have a valve, and be sized so it can take at least all of the overflow of the tank, i.e., under full siphon. In full siphon the entire tube is full of water and contains no air. In this model, you can adjust the valve to balance the overflow with the intent that the lower pipe runs full all the time and thus silently while the other higher standpipe is empty and takes very little water or simply takes small amounts.
The second pipe will take any surplus over flow and act as an emergency pipe in case the lower standpipe is clogged or stopped. The valve in the lower pipe will let you balance the flow to reduce water discharge noise.
If you have 2 tubes acting as described (both making noise and both open), then it sounds like they have the same level (not how the linked design works) and that there is no valve. It's also possible that both tubes are too large for the intended overflow, but if they are the same level, you may get the gurgling even if they are correctly sized for the pump.
I haven't built one of these, but I suggest you post a picture as it will certainly help others who have built these.