I didn't notice much of a slowdown with the new firmware, but since I don't have 2 machines to compare side-by-side, that may be just because I don't have anything to compare it to.
Skip works OK for me with MTPCenter and UPnP. What server are you using?
Also, for the Dolby downmix: If you're using the Pinnacle server, there is an unlock that you can do through the server itself. If you aren't using the Pinnacle server, there is this workaround.