Hi borth,
App Inventor use the built-in Android WebView component for the web viewer, so I would expect that this issue might affect any app that uses that particular widget. That being said, here are a few things you might want to test:
1) Does disabling either of the frameworks stop the autoscrolling behavior? If so, that might indicate a bug in that framework.
2) Does your phone have the Android System Webviewer package installed and is it up-to-date? Some users have reported issues where the App Inventor webviewer does not render pages with the most recent update. Maybe the behavior problems are also related?
3) Use a tool like AppToMarket to increase the minimum SDK to a higher value, e.g. 14. This will replace the default webview implementation with a Chrome-backed version on most phones, which may solve your problem.
4) Check whether or not you are using a combination of Scrollable on the screen and Fill Parent on the webview. I could imagine a scenario where the page is resizing its content and that might cause an effect that looks like scrolling but isn't.
Let us know if any of these checks helps,
Evan