cold bottles and slow fills. if it foams you have to waste beer until you get liquid (not foam) at the top. I know that they may be obvious and you've probably taken care of it, but make sure that you bleed the extra pressure off the keg before filling.
Cold, wet bottles seem to work the best...very low psi for slow fills. I got my best results when chilling the starsan solution and dumping bottles in there for a cold wet bottle.
I put my bucket of iodaphor solution in the chest freezer the morning I'm going to do some fills. Throw the bottles in the solution as well as the beer gun. By the time I get home, everything is the same temp. As noted, you need the bottles cold to avoid the foaming.