I found there are several config files for SL2 on Windows, one in:
%AppData%\Sublime Text 2
and another one in
%SublimeText2InstallPath%\Data
So, which config files is used on Windows? and what is the purpose of having multiple copies of them? I find starting SL2 from the right-click context menu, running the .exe directly, and starting it from command line results in different configuration file being used, not sure what caused it. how do I set it so that it only uses just a single set of configuration files?
Take a look at the Sublime Text Unofficial documentation page.
EDIT: Since I see this is/was a link only answer, here's the relevant text from that webpage:
Sublime Text will look for resources inside the packages [emphasis mine] folder. We’ll talk at length about packages later, but the short version is that, to keep things tidy, Sublime Text has a notion of a package, that is, a folder (or zip archive) that contains resources that belong together (maybe they help compose emails faster, write HTML efficiently, enhance the coding experience for C, Ruby, Go…).