The free edition of phonegap build only allows one app. You should login to phonegap build and delete the current app: this will allow you to create a new one from our platform portal and continue.
Have you tried selecting 'Do it yourself', instead of 'Build in cloud option'? This works better in my experience. After that just create a new project via http://build.phonegap.com/apps and upload the zip file yourself.
You could try these two links to see if this is your problem. I think the problem is phonegap related and not Mendix related. http://community.phonegap.com/nitobi/topics/privateapplimit_reached