It also looks like you've got your disks set to dynamic, which may be the reason you're seeing these changes.
There's more information on basic/dynamic and primary partitions on this link (more than I can explain in a post). It highlights the changes in dynamic disks and some of the benefits (for example, software RAID and spanned volumes).
http://msdn.microsoft.com/en-us/libr...(v=vs.85).aspx
With dynamic disks, there's no need for "primary" and "extended" partitions ("simple" dynamic volumes are the "primary" equivalent) - so I wouldn't worry about the change. However, there probably isn't a reason for you to use dynamic disks (as far as I can tell), but it won't do you any harm.
Don't worry about your flash drives - that's normal