That is Windows running things listed in your RunOnce key(s) in the registry.
One of them probably just took longer than expected, so you got to see the actual RunOnce.exe window.
EDIT: A little more info:
From here (Bing-translated to English):
Perhaps the most important moment of this phase is the automatic execution of programs present in the key of registry HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnce. These programmes are implemented, as its name suggests, only once: at the time that a user with administrative privileges, log on to the machine. There is a programme responsible for carrying out this process: C:\Windows\system32\Runonce.exe. Called the "Runonce.exe /Explorer" command, which, if the user is Administrator of the computer, is responsible for executing the contents of the key RunOnce (which usually are downstream of the installation of a program).
From what I can tell (there's not much info on it), the "/Explorer" switch is what causes RunOnce.exe to be run against each entry in the keys.