Jester: when you write "For some reason when I shut down I get a bunch of "VBox Drive" or something that didn't appear before" I am guessing that somewhere back there you installed a Virtual Box, maybe for the free Sun Virtual Box machine, and now it won't go away. I did that months ago, and it messed my machine up until I removed the VBox files manually. You could maybe go look for them (search for "VBox") and delete the folders containing the files.
best
John Tranter