I've just checked the release notes from AVCHD Presents and they credit the WG releases so you're absolutely right about the source material.

My WG transfers are siting on my redundant HTPC (redudant since my PS3 took over my media stuff) but I was due to be dusting it off and hooking it up to my suround sound system so if nobody else confirms, I'll see if the audio track is absent in Eps 1 and 2.

That aside, it would be fantastic if Eps 1 and 2 could be re-encoded with the audio fixed in AVCHD but I agree, it's a lot to ask.