This has been an issue since wordpress multisite 3.4. We are now at 3.6.1. This has been unresolved since then, and I would like to see a fix.
Read all about it there. I've searched endlessly for a REAL solution, not a workaround. The work around is to uncheck option 4 in the domain mapping settings. However, this option is highly desired. Why has this been broken for so long?