I see these encoded in my test system also. From what I understand of WebDAV, encoding these shouldn't cause an issue. I presume both values function the same?
UPDATE: I understand that parenthesis' are classified as sub-delimiters (W3C) so I wonder if they need to be treated differently as part of a URL as with being part of a set of URL Parameters.
Point taken on the pain of doing a direct comparison of file content post upgrade during a file comparison - I guess you'd have to change you checker to account for specific (non-impacting) encoding differences.