I had the same Problem, but did not use the WP-Amazon Plugin.
For me, this was caused by the Plugin Simple Tags. I already wrote to Amaury about this.
Deactivating it did the trick. I suppose some Plugins that hook into the Writing screen in Admin Panel use javascript functions, and perhaps a variable is named the same. Stuff like that. I am not a Javascript master though.
So if you experience problems with the media uploader popup, look for plugins that add functionality to your writing area.
regards,
Jan