I think you might need to be a little more specific.
If you mean that during use, and with plenty of water still in your barrel you are still getting air in your system, then your problem will be at the joint where the the hose from the barrel enters your pump box.
OR rather it will be on one of the joints between the barrel and the pump.
At one of these points you are drawing in air, causing the pump to work poorly.
You have to be sure that at these points everything is spot on.
When the pump starts to go wonky, keep the brush head close to you and experiment by pushing the hose in really tightly at these points.
Eventually you should find the point at which air is getting into your system and then be able to rectify. Either by replacing the joint or ensuring that the hose is properly seated.
I have a similar system and had this problem myself! I have always ran my barrels completely dry too, and no problems in 18 months of constant use.
My own system is Peter Fogwill's trolley system, which works in much the same way as Matt's DIY one (even if it does look different!)
Regards,
Ian