You'll never be able to get all the crap out of your gravel. I have sand in my mbuna tank, and as soon as I syphon all the poo off the surface, they all start crapping at once (I swear it's a conspiracy) and by the time I'm done it looks like I've never cleaned at all. Ok, I'm exaggerating a little bit, but it's a never ending cycle, clean, poo, clean, poo. Just a part of the joys of fishkeeping. As long as you are syphoning the gravel regularly, and your nitrates aren't spiking, don't worry about it.