Dave,
After looking through my code, I found out why it wasn't working (logic failure on my part) and the code does what it is supposed to do.
However, I see now that the pdf must have commenting enabled to save settings correctly in Reader 9 (9.4.1).
Reader XI prompted to save automatically if I changed the setting even if the file was not saved as Reader extended for commenting.
In any case, thanks for pointing me in the right direction.
Do you know if multimedia_saveSettingsString and multimedia_loadSettingsString are officially documented? This has not turned up in my searches so far.
I would still be curious to see the actionscript code you used to compare notes.