That dialog needs a little tuning.  The theme will get applied automatically when selected.  Saving is for the other properties.  I will change that word from save to ok/done so to avoid confusion.

So, I suspect that these issues will go away when we introduce a set of default themes in Brackets.

So, I will go through the process of cleaning out my entire environment and set stuff up from a clean slate to clean up all these lingering issues.