I had a similar problem when I was starting a new city in an undeveloped region. Basically, whenever I connected to SimNation (it didn't matter where on the map I did it) my Sims stopped commuting and abandonded their homes. When I destroyed the connection, they came back and went back to work. Since then, I get that problem every now and then in my other cities in that region, but not nearly as much as I did in that first city. I'm thinking that one of the NAM plugins was the cause of my problem, because I had just installed it and had never had that problem before. But you never know...