Please disregard. I'm working with Scott Musser who is helping us with the issue. He was able to show us how to verify which version we submitted. I will get the correct package submitted and will update this thread once I've verified with debug information that the correct package was submitted.
It is unfortunate that the review team dropped the ball on you in April - if they did not email you back then re bundle not updated. Things like that shouldn't slip. I am trying to figure out myself what is a way to moving things forward without being overburdenly / desperately pushy.
Regarding self-help though, consider showing somewhere the channel version ("About" screen?) and fetch the number to show there from the manifest file with roAppInfo.GetVersion(). That way you can always check with the remote that indeed the channel is the one you wanted it to be.
There is one nasty caveat to that - the version# showing in the Channel Store (the info screen when clicked on an icon) differs from the version# from the manifest. This version is taken from the web portal description. It doesn't make sense to have 2 separate numbers but i guess it is unfixable because of the way they handle the bundles.