1. why is the device internal storage cache out of date?
2. how do I force it to update to have the CORRECT list of files that you can see in Root Explorer if you go there on the phone itself
3. how do I ensure I've actually grabbed all the files I told it to grab?
4. Is there any other solution for this?
5. Has anyone else experienced this or am I an idiot?
I'm on stock ROM and having no end of problems with this. This is just like google, introduce some new feature but don't bother fully testing it. The phone appears to maintain an internal cache of the files and folders on the phone, which sometimes is out of date. It reports this list to the your computer when you connect it. Several times now I've tried to copy off or backup select folders that had files I needed and the cache was out of date so Windows Explorer didn't know there was a file there to request a copy of.