I looked into this some, and was unable to replicate any issues with this.
However, looking more into your startup log, it seems to have a few “broken” files in your Packages/ folder.
ignored_packages: ["Vintage"]
unexpected rule type, was expecting one of match, include, begin or patterns, got: {comment: Note how all @rules are prefixed.}
generating syntax summary
generating meta info summary
Unable to parse binding {cmomand: wrap_zen_as_you_type, keys: [ctrl+shift+a]}
top level value must be an array
ignored packages updated to: ["4GL", "ActionScript", "AppleScript", "ASP", "Batch File", "C", "C#", "C++", "Clojure", "D", "Diff", "Erlang", "Go", "Graphviz", "Groovy", "Haskell", "Java", "LaTeX", "Lisp", "Lua", "Makefile", "Matlab", "Objective-C", "OCaml", "Pascal", "R", "Rust", "Scala", "TCL", "Textile", "Vintage"]
You’ve got at least one broken .tmLanguage file: (unexpected rule type, was expecting one of match, include, begin or patterns, got: {comment: Note how all @rules are prefixed.}).
You’ve also got a broken key bindings file (Unable to parse binding {cmomand: wrap_zen_as_you_type, keys: [ctrl+shift+a]}).
The issue with the broken syntax may be causing issues with Sublime Text caching the compiled forms of the syntax definitions.
Generally you should not see ignored_packages: and ignored packages updated to: before pre session restore time:.