Crazy, what kind of set up were you trying to do there? Been using it for probably 10 years and I can't remember the last time I had an issue and I run updates on it automatically every day. Biggest problem I remember is having to chown a directory again or something.

It usually hit, when a dependency of programs gets shoved out into cask. The moment where that happens, and where the things listing it as a dependency realise its now cask and not the main repo, is not altogether in sync.