Try rendering to a lossless codec. MP4 can be very problematic in AE.
Tru opening your aep in Adobe Media Encoder and rendering your MP4 there.
Also, we have no info about your comp. it could be the wrong size for MPEG. It could have other problems.
I tried that and it didnt work but now it says Frame Size Input error (512), even though all my layers frame rate is at 59.94 and im not using any video copilot plugins, i dont understand whats wrong.
Well, the short answer would be that you have a CoDec pack like K-Lite on the system and it's making a mess of your otehr CoDecs. Get rid of it, reinstall AE and Quicktime. If that doesn't seem to be the problem, then we need more info like exact render settings, comp settings, what source footage is involved and what not...