I had a similar problem when I set up our new tap systems. I beat my head against the wall for a week before I solved it. I used barb-splices to join my choker lines (3/16" ID) to the beer trunk lines (3/8" ID). The barbs I used were slightly smaller ID than the choker, and were making a venturi where the beer entered the choker line. Any restriction in the lines with a larger ID downstream of the restriction will do the same, as the pressure abruptly drops after the restriction, causing the beer to "break" and foam.
I replaced the barb splices with properly sized ones, and the problem was solved.
We're also running 2 staions/keg, but using beer pumps and long (~45') beer trunks. Balancing the two lines was just a matter of adjusting the length of the choker lines on the shorter run.
Terminal Gravity Brewing,