We are trying to use CCRenderTexture similar to the test that is included with the cocos2d download, but we are having problems with the alpha channel. There is a screenshot and code posted below to reproduce this. This was built using 0.99.4 - on simulator and device (iPhone & iPad). We found even if we put that gray background in the rendertexture test instead of letting it be black, we see the problem there too.
CCColorLayer *background = [CCColorLayer layerWithColor:ccc4(200,200,200,255)];
[self addChild:background];
CCSprite *spr = [CCSprite spriteWithFile:@"fire.png"];
[spr setPosition:ccp(16,16)];
CCRenderTexture *rend = [CCRenderTexture renderTextureWithWidth:32 height:32];
[rend begin];
[spr visit];
[rend end];
[spr setPosition:ccp(50,50)];
[rend setPosition:ccp(100,50)];
[self addChild:spr];
[self addChild:rend];
