I found out what is causing the problem.
startScene method by adding this code to the end of AppDelegate didFinishLaunching:
CCDirector* director = [CCDirector sharedDirector];
CCScene* main = [[MainScene alloc] init];
I needed for my specific reasons. Can I fix something in cocos2d source code to fix this?
Update: I've found a hot fix for this, changed this line in CCDirector runWithScene
[self performSelector:@selector(drawScene) onThread:thread withObject:nil waitUntilDone:YES];
Can somebody tell me is this a safe replacement?