Android WebView VS Phone Browser

This article outlines your speculation about stock browser differences between manufacturers, that absolutely is true: 5 reality checks every team needs before working on Android webkit

…which does cause trouble and mysterious/difficult to diagnose/solve problems.

As far as your issues with your WebView implementation:

Version of jquery-mobile may be an issue jquery-mobile loaded into an android WebView if you are using jquery.mobile-1.0.1.min.js you may want to try the uncompressed jquery.mobile-1.0.1.js

And Flash :-/ Good luck:
Screen blinking when using a webview with flash

Flash in WebView not working on Android 3.2

Flash video not displaying in WebView for Android 3.0.1

For loading SWF:

Load an SWF into a WebView

loading flash files (.swf) webview in android

Good luck with that, seems like a lot of variables with devices, Android versions, etc. And will take persistence with trial/error.

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