The server at ai2.appinventor.mit.edu doesn't handle large numbers of assets. Writing each asset redundantly take time and so you likely are pushing the upper limit of the allowable runtime (Google's servers forcibly kill the process at 1 minute of runtime).
We haven't updated code.appinventor.mit.edu yet to run the latest release while we spend some time working on outstanding bugs. If you haven't used any new features of the release, your old AIA should still work in spite of the warning you receive about it coming from a newer version of App Inventor.