When using a resource pack with a custom Mojang logo, it does not work. It only shows the default Mojang logo. Watching the game output as the game starts, I see that it says "Created: 1024x512 textures-atlas" after the Mojang logo appears, which may be the issue. If the textures-atlas were created before the Mojang screen loaded, then it would work properly.

This bug does not occur in the OptiFine client. I think the Optifine devs fixed this bug. But Mojang hasn't fixed this bug for their original client. Please fix it, I like using a cyan Mojang logo which I put in my resource pack!

Also, this bug has been around for a long time, but I think nobody has addressed it because they think that this bug is intended.