OK, instead of a drag & drop to open the sketch... Almost for sure the Linux version of Arduino will let you open it by browsing to it. This will sound a little bit paranoid but I would delete a semi-colon or something to cause a syntax error in one of the files. I've had problems with Arduino using what ever I last opened and having it build the wrong thing. If you cause a syntax error in one of the files, and it complains about it during the build, at least you will know its working on the right code base.