[Bret Williams] “What a mess.”
No doubt. There are a long list of gotchas with Red.
Again, were the proxy files made with RCX, or where they shot at the same time and recorded in camera?
Sometimes, the format of the media card in the Red can screw this process up (Fat32 vs UDF).
Usually RCX can relink to all the media, though, without the freeze frame.
Another process to try is to make a duplicate timeline in FCPX, strip out all the audio and unnecessary footage (like anything that is not Red originated) and try it on an audioless XML and see if that works.
That should get rid of your sync’d clips too.