I've just been to the Apple store. But without seeing or locating the error message also the guy there couldn't help me. But he recommended to keep 'Console', which you find under your Utilities, open. And to try to narrow the time window down in the moment the pop-up window occurs.
As soon as I came home the window actually appeard immediately after I logged into OS X.
So I went into the Console and took screen shots of everything that happend within the 2 minutes when I switched the machine on and opened Console.
Indeed, Console is displaying some error message of drivers which are unavailbe of an old audio interface.
But I don't think that's the issue. I think it might be related to sound audio stuff like plug-ins.
But I guess I will know more when I take that data / screenshot to apple next time.
Hope that helps!