Just checked final version 3 (as demo) and the problem still exists.
If by "the problem" you mean the fact that the materials are not saved in the proxy, then yes - it still persists. This is because we cannot save the materials there until we decide upon a common format for the materials for all the host applications - 3DSMax, C4D, Archicad, and all the possible future ones... This is a major decision that we need to think through to make future-proof and that will also need large changes in the proxy import/export code in all the plugins. We want to do it eventually, but I'm afraid it's not something that will get into the plugins in a few weeks or so.
If you mean some other problem, could you please be more specific? We would like to help you and fix it.
P.S.: As I am reading through the thread again to make sure I didn't miss anything, I figured that my comment about fixing the issue was badly worded and could be misinterpreted ("Hi, we found out the issue and fixed it"). We fixed the problem with some missing texture assignments in the proxies, which is what I originally thought that this thread is about. But you probably meant that the proxies don't save the materials inside themselves, am I right? If so, then I'm sorry for the misunderstanding.