Well, since the last alpha/beta I also got the black screen with small red rectangle at startup that disappears after a while and then I get the Ubisoft logo. Everything works just fine in game etc. I thought it was some new 1C splash screen etc that had been missed in the latest build?
Anyway - no problems in game otherwise and the mini fix did not change it...
Running a 580GTX with the latest GeForce 301.24 Driver BETA
EDIT: Vote for the black screen with red rectangle at startup in the bugtracker:
http://www.il2bugtracker.com/issues/239