The issue was mostly my bad programming with the UI thread and other things.
I was collecting items with SAXParser using AsyncTask and adding items to a
subclass of ItemizedOverlay. I was calling the populate method for each
added item instead of only once when all items are available (read the fine
print for ItemizedOverlay.size()). Another issue was setting a button text
in the AsyncTask.doInBackground method.

I think in the end, being able to breakpoint the Android source would not
have helped me with multi-threaded debugging.

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