I am not sure why it happens but my gut feeling is something to do with the Fat32 file system mixed with the XMB as that is the only thing I can attribute to the oddness.
One thing I do recommend trying to find is a external HD with an auto on/off feature via usb. So it just detects when the ps3 is on or off and turns itself on or off accordingly. Its much easier than dealing with the drive constantly by hand IMO.
Just download some porn to fill that free space up...that shouldn't take too long
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edit: I just realized, when I ordered my external drive I never even considered the fact that the ps3 might not accept such a large drive...guess I got lucky
. Smart move thinking ahead J.