I am having this same problem. I have set atomic_save to false in my User/Preferences.sublime-settings file, restarted ST3, restarted my computer, and yet every time I create a folder or file from within ST3, the file has permissions wide-open. This is causing some problems in my workflow, as tools important to my ability to develop require the directory they operate on to have file permissions of either 755 or 775. So I'm working around it by making sure I create all folders and files first, and then open them in sublime, but this is definitely not how I prefer to work. I've been a long time fan of Sublime, and encouraged a number of my friends and colleagues to switch over, created multiple plugins, etc. but this is a real problem with serious implications, so I really hope getting it fixed is a high priority. I know you said it will be fixed in the next build. @jps Is there any idea how far off that is? I want to remain on 3, because it really is a huge improvement over 2, which was already an amazing editor.
If It helps I am currently on Ubuntu. These are the packages I have installed:
"Color Scheme - saulhudson",
"Enlightened Color Scheme",
I have tried disabling all of them, with no change. Thanks for all your hard work, I'm sure you will get this sorted out quickly.