Hi Bruce,
Based on the error, I would have to say the forms authentication timeout is occuring, which is different from the IIS executionTimeout.
Look for:
<form>s name=".DOTNETNUKE" protection="All" timeout="60" cookieless="UseCookies" />
And adjust the timeout (in minutes) to your needs. e.g., above is a timout of 60 minutes.
Also, check your application pool settings and make certain it is not automatically recycling the worker process during the upload timeframe.
Hope this helps.
Rob