Can you share your App ID, and I can have a look at your app? PM if you'd prefer.
Have you tried creating a new app on build?
App ID is 996958.
I've been creating it on Phonegap Build for a while now. I've uploaded many versions. It has been excellent up until just recently. I'm not sure what's going but it seems like there are 1 or more kooky things happening that may be affecting each other.
I'm fairly positive it has nothing to do with the codebase unless there was some major update where I needed to change things and missed it. I published a release within the past month (I think) and everything was good. The past few days have gone haywire as per that other link in the thread.
Looking at the file tree output of your zip, it looks like you have a second www folder nested in your app, which likely has an old copy of your app. The build system could be (erroneously) using that wrong nested www. Could you check through any nested folders in your zip? Or send your zip to firstname.lastname@example.org so we can have a look at it?
Not sure how the heck that happened.. but that seems to be it. Someone must've accidentally dropped the www into the compilation folder or.. I'm not even sure what.