I have found a bug in the LaTeXTools plugin whereby it overrides a particular setting every time the plugin is loaded under Linux. I believe the intention is that this should only happen the first time the plugin is run. I have corrected this behaviour in the attached patch, as a result it is now possible to change this setting if required (for example I use rubber rather than latex or pdflatex directly).
oops. it loos like robthebob already committed this in 2010 and so it's been fixed since then. But I made some small changes to it.