Ian,
Thank you for giving the product a try and reporting these issues. We'll be hard at work monday to fix whatever issues come up and try to get an update out quickly to address any problems found.
It sounds like we didn't do enough testing with updating from older versions and reapplying, so we'll get on that first thing and make sure these problems are fixed quickly. Thank you for your patience and please let us know whatever you find and we'll make sure to get it resolved.