I've had these kinds of problems as well, but not only with linux, windows as well. Whenever it happens, I usually just use my hot-keys to get back the original machine that i was working on at the time, mouse the mouse around a little, hit a few keys, then try again. That usually "resets" it...
I'm not very familiar with Linux either, but I'm trying to do this exact same thing, only my SATA Controller is built-in to my motherboard (ASUS A7N8X-Deluxe). Now, the controller that Asus has put in there, is a Silicon Image 3112 SATA Raid controller. You can get that exact same version in a...
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