For that problem, i really don't know what happens.
The "splash" screen you are speaking about, is just the black screen with one line in white at the top saying the version?
There is absolutly nothing in my code that could need you have to press control key. this screen just stay here 1seconde.
Can you try this :
Change you windows desktop color depth in 65535 color (16 bit / pixel)
And in your config file , locate the row : WINDOWMODE=NO , and change it to WINDOWMODE=YES , and run Atomic again.
Atomic will start windowed , but if another popup or application or dialog appear in windows that could stuck Atomic waiting a CTRL key, it will appear i think. Let me know , if you see something.
thanks