A bit difficult to explain, but I'll give it a shot.
When you run a new instance of sublime_text.exe with the --new-window command line option it uses the current working directory of the previous (first) sublime_text.exe instance.
Is there a way to fix sublime text so that subsequent instances opened set the correct current working directory (the directory sublime_text.exe --new-window was executed from)?
Failing that is there a way to set the current working directory via a command line flag?
I hope I'm making sense here.