Avoiding Deep Collisions

Any tips for this situation, as I'm a bit stuck as to what to do

I'm simulating the flow of particles through a tube, with the physical controller. The particles have a radius of 1.8, and the tube has a radius of 4. Hence, you can squeeze about four particles alongside each other in the tube. I'm using periodic boundary conditions to recycle the particles, so that they are repositioned at the start of the tube after they pass out of the end. Each particle has a large force acting in the direction of the tube, and small random force perpendicular to the direction. The simulation will normally work ok, but occasionally a particle gets stuck at the start of the tube, i.e. it bounces around at the entrance without making any progress along the tube. Once other particles are repositioned at the start, they get caught up with the errant particle, and make no progress either. Breve prints loads of collision depth warnings, so a guess deep collisions are going on. Any suggestions on how to avoid this behaviour?