Googled for "Configuration Test Protocol (loopback)"
Ended up at:
http://wiki.wireshark.org/Loop
It looks like it's part of a spec that some people implement (Cisco) and some don't. You aren't going to be able to do much to stop it. It doesn't look like it's something that's SUPPOSED to be bridged by Linux bridging code. Most likely, you have a router somewhere that's generating these packets and Linux is just plain ignoring because, as that link says, it's not "real" Ethernet but a hangover from an earlier design.
To be honest, I don't think that there's much you can do. And nobody is really going to notice an obscure protocol like that being "missing". They'll think you've just turned off the option in your router.