I’m also seeing this, although I haven’t found a reliable way of reproducing it.
installed packages: ["0_package_control_loader", "AdvancedNewFile", "Alignment", "AlignTab", "AppendSemiColon", "Better CoffeeScript", "BracketGuard", "BracketHighlighter", "ChannelRepositoryTools", "Color Highlighter", "DocBlockr", "Edit Preferences", "EditorConfig", "Fold Python Docstrings", "GitGutter", "GitSavvy", "INI", "JumpTo", "LaTeX-cwl", "LESS", "Markdown Preview", "MarkdownEditing", "MarkdownTOC", "Origami", "Package Control", "PackageResourceViewer", "Plugin Debugger", "RestructuredText Improved", "Sass", "Schemr", "ScopeHunter", "SCSS", "SideBarEnhancements", "Stylus", "SublimeLinter-annotations", "SublimeLinter-contrib-mypy", "SublimeLinter-contrib-sass-lint", "SublimeLinter-flake8", "SublimeLinter-javac", "SublimeLinter-lua", "SublimeLinter-pydocstyle", "SublimeLinter-pyyaml", "SuperPython", "SyntaxHighlightTools", "Table Editor", "TestPackage", "Theme - Freesia", "Theme - Nil", "To Hastebin", "UnitTesting", "Wrap Plus", "YAML Nav", "Zeal"]
packages: ["AlwaysEnsureNewlineAtEof", "ASCII Decorator", "Babel", "backrefs", "BracketGuard", "BracketHighlighter", "bz2", "CSS", "CSScheme", "Default", "Diff", "File History", "HTML", "InactivePanes", "INI", "InsertDate", "InsertNums", "Java", "JavaScript", "Jedi - Python autocompletion", "Language - English", "Language - German", "LaTeX", "LaTeXTools", "Lua_user", "Makefile", "markupsafe", "mdpopups", "NewPackageDev", "Open-Include", "PackageDev", "PackageResourceViewer", "PHP", "PlainTasks", "Plugin Debugger", "pygments", "Python", "python-jinja2", "python-markdown", "PythonImproved", "pytz", "pyyaml", "QuickRulers", "Regular Expressions", "RestructuredText Improved", "SaneSnippets", "SCSS", "SendSelfTest", "SideBarEnhancements", "SublimeLinter", "SublimeLinter-contrib-mypy", "SublimeLinter-contrib-sublime-syntax", "SublimeLinter-flake8", "SublimeLinter-jshint", "SublimeREPL", "SyntaxHighlightTools", "Theme - Nil", "TodoReview", "Troubleshooting", "User", "VisualIndent", "YAML", "YAML Nav"]
ignored packages: ["Babel", "BracketGuard", "Color Highlighter", "Markdown", "PythonImproved", "RestructuredText", "Stylus", "SublimeLinter-lua", "SyntaxHighlightTools", "Theme - Freesia", "Vintage", "YAML 1.2"]
packages managed by Package Control: ["AdvancedNewFile", "Alignment", "AlignTab", "AppendSemiColon", "ASCII Decorator", "Babel", "Better CoffeeScript", "BracketGuard", "BracketHighlighter", "ChannelRepositoryTools", "Color Highlighter", "DocBlockr", "Edit Preferences", "EditorConfig", "Fold Python Docstrings", "GitGutter", "GitSavvy", "INI", "Jedi - Python autocompletion", "JumpTo", "LaTeX-cwl", "LaTeXTools", "LESS", "Markdown Preview", "MarkdownEditing", "MarkdownTOC", "Origami", "Package Control", "PackageResourceViewer", "PlainTasks", "Plugin Debugger", "RestructuredText Improved", "Sass", "Schemr", "ScopeHunter", "SCSS", "SideBarEnhancements", "Stylus", "SublimeLinter", "SublimeLinter-annotations", "SublimeLinter-contrib-mypy", "SublimeLinter-contrib-sass-lint", "SublimeLinter-flake8", "SublimeLinter-javac", "SublimeLinter-jshint", "SublimeLinter-lua", "SublimeLinter-pydocstyle", "SublimeLinter-pyyaml", "SublimeREPL", "SuperPython", "SyntaxHighlightTools", "Table Editor", "Theme - Freesia", "Theme - Nil", "To Hastebin", "TodoReview", "UnitTesting", "Wrap Plus", "YAML Nav", "Zeal"]