Changes to the MythTV communications protocol require a change to the protocol version. This is most commonly noticed when running different versions of a backend and frontend. MythTV does not support running different protocol versions between a client and server.
If you experience a protocol mismatch, you need to be sure all your systems are running the same version of the software. If you are using a development branch like trunk or the fixes branch, be sure your systems are all running the same revision of the software as the protocol version can change within a development branch before an official release tarball is made.
Many package maintainers (rpm, deb, ebuild) build packages from the fixes branch. This means that they are distributing an unreleased version of the software. Official releases are distributed from www.mythtv.org as a download.