I'm usually bothered by ST2 looking for source files that aren't there, since I don't keep them in Dropbox...
Well, YMMV as usual I guess :P

Actually I'm using the same files for both machines, they are sync'ed with the help of the mighty Dropbox (see this for reference ==> http://userecho.com/FFB8 )

Actually now I see that there are some per-platform default preferences files ('Base File (Linux).sublime-settings' and 'Base File (OSX).sublime-settings') and they carry mainly font settings.
Maybe there will be the possibility to access them from the menus (I'm on OSX now and I can't seem to find them).