So I found the problem in the legacy cbin proxy loader and fixed it. There are still some other things we need to do before we release another daily build though, so it for sure won't be today. Once the daily is out you can work with it directly or you can just use it to convert your cbin proxies to cgeo ones.
At this moment the workaround is like I said. Load your cbin proxies and convert them into cproxy using corona 1.2.x. Those will work in 1.3 just fine and you won't need to convert them any further.
Regarding the format change. With cgeo we took the time to think about the extensibility of the format which was not the case before. So hopefully, we won't need to change the format (i.e. extension) for a long time.
Cheers,
Robin