Air in ballast system

Well I just completed my ballast system on my 1992 Nautique Excel. I opted for the Ballast Puppy approach and tied into the raw water intake. When I finally got to try it on the lake, the Puppy was pumping about 25% air into my fat sacks instead of water. This became really annoying because I kept having to burp the bags, which pretty much eliminates the advantage of a self contained ballast system. I redid the initial "T" so that the pump was below the water line and below the intake line, but air is still getting in some how. Has anyone else had this problem and if so, how do you fix it. I have redone the setup so that the bags are filling from the back, which makes burping them much easier since I can get to the plug, but I was hoping to not have to do it all. Any input you have would be greatly appreciated.

I have the puppy's also. I had to burp the bag the first time I filled them up. Air in the lines. But after draining them the bags shrink up like raisins and there is no air in them. try filling the bags all the way. Get the air out. drain the bags using the pump, and fill again to see if air gets into it.

You could just add an air vent line to the bags.
I think most stock ballast systems have vent/overflow lines - I know mine does.