Anion-cation balance in particle phase
Yes, you have left out one very important cation from your cation/anion balance: $\ce{H+}$

The primary pathway for new particle formation in the atmosphere is the photo-oxidation, via hydroxyl radicals, of volatile reduced sulfur species to form very non-volatile sulfuric acid.  For the most part then, new particles start out as puny droplets of sulfuric acid and grow via accretion, etc. from there.  

I recommend measuring the pH of the filtered aerosols, and I strongly suspect that will account for your missing cations.  

If I have missed the point of the question, please feel free to ask for any clarifications in the comments.