My theory is as follows: Sam's problem is not that his hard drive (or his soul/memories, pick your poison) has been psychically/psychologically corrupted, or somehow physically damaged. Rather, it has something to do with his networking and his Domain Name Server settings (insert Show-related metaphor here). This creates some kind of horrific tangle deep inside his hard drive that eats all of the memory and disrupts the overall functioning of him.
When these various things are dragged to the Trash and a brief Disk Permissions Repair is instated, he's back in black, or... aluminum unibody, or whatever.
Come 7x23, I predict that Sam will be fine, we'll all (writers included) be kind of confused as to what the problem was and how it was fixed, and the actual logical progression of all this will be somewhat muddled. Then we'll scratch our heads and shrug and decide, eh, we're cool with it. Can't look a gift horse in the mouth, after all.
My spoiler source? THE APPLE STORE. Watch this come true anyway, bahaha. XP Personally, I'm 60/40 on the "and this will all be solved", and 100% on "we'll all be kind of confused."
Also, earlier I was troubleshooting Samputer's new symptoms and talking to my dad about an error message I'd seen in Console, involving sibling directories and such. His response?
"Metaphorically speaking, it would be interesting if Samputer is having invalid sibling link problems. My guess is that the only way to get Lucifer out of Sam's noggin is to replace the hard drive."
stressed and aggravated!kalliel --------> wow how is the world this hilarious!kalliel