Remember, Windows uses CR LF to end a line, OSX (and Linux) uses just LF, Since you use both clients, that might be an issue.
I have never had a RULE reformatted. However, I always see a query get reformatted. I wish this would be fixed.
I understand if any attributes are added / deleted, it might break an existing query text. But if I just go in and change formatting, or Label, I wish it was not rewritten.
Just my 0.02 cents worth.