Ok, so I got my Harmony 1000 working. I spoke with a tech in tier 2 support. Basically, for now he said that any time you are going to be updating the 1000, launch the program using the shortcut they provide. (For you dealers out there don't manage your Harmony 1000 accounts through the website.)

Just click the Harmony desktop and you will be good to go.

A new verison is coming soon and after it is release you will be able to manage account through the dealer site.