I installed Package Control on SB3 3059 on a Mac Maveriks with all patches.
Installing a Package with Package Control, I get the following behaviour:
Installed SidebarEnhancements (works fine as expected)
go to Sublime->Preferences->Package Settings->Sidebar->default
The default preferences get displayed as expected
Save them outputs the following error message in a msgBox:
Unable to save ~/Library/Application Support/Sublime Text 3/Packages/SideBarEnhancements/Side Bar.sublime-settings
Error: No such file or directory
But with some packages SB3 crashed completely with this.
It seems the packages default settings are not beeing saved to the default location at install, so they're not present as expected by sublime.
I'm not sure if this issue is related to Package Control or SB3, so feel free to point me to PackageControl in case I'm completely wrong here.