Ok... so now I can draw a conclusion.
Also on my other system the slowdown is not present... Or (to be more accurate) it is but it's not noticeable. A 2-3 seconds slowdown is liveable... in the past the slowdown lasted at least 30 seconds.
Why? Well, although the ngen service is set on automatic, an it starts at windows logon, it immediately stops. Why? This I don't know.

Maybe it's something Microsoft has done, maybe the -ai -fo arguments has something to do with it.
And btw, when I type that command, only the c:\windows\microsoft.net\framework\v4.0.30319 windows opens in full width and then restores down (shrinks down). So there's no message I can report.
