SQL operation that takes longer that 30 seconds is very strange, and I’m sure that increasing the timeout will work fine for this case. I’ve read that read uncommitted isolation level exists on SQL Azure, so it seems to me that timeouts are caused by overloaded database instance.
This timeouts may be also caused by old expiration manager, if you have many expired records (fixed in 1.3.2). But it may also be caused by the main application itself.
Thank you for the tips on SQL Azure!