Are you sure your second partition is not protected? Are you shutting down cleanly or hibernating?
If you're using HORM then you need to unmount your non-EWF partitions before hibernating. See here for how to do it using diskpart: http://social.msdn.microsoft.com/For...7-d3940b370b50
Or here for doing it programmatically: http://msdn.microsoft.com/en-us/library/aa460084.aspx
I used to have a CLI tool to do this. Might still be available on the forums I think I posted it years ago.