I'm experiencing the same issue (Ubuntu 12.04), but seeing no such errors on the console from which Sublime is invoked.
In fact, with --debug, I see this:
$ ~/bin/Sublime\ Text\ 2/sublime_text . --debug
main.cc:1283 main startup, version: 2210 linux x32 channel: stable
main.cc:1297 main executable: /home/ben/bin/Sublime Text 2/sublime_text
main.cc:1298 main working dir: /home/ben/tmp/puz
main.cc:1299 main packages path: /home/ben/.config/sublime-text-2/Packages
main.cc:1300 main settings path: /home/ben/.config/sublime-text-2/Settings
main.cc:1345 main Passing command line to existing instance
which would suggest to me that single-instance mode is working ok... but it still creates a new window.