After Effects - Render quality

Okay so i'm relatively new to after effects and in my previous project i was using an AVCHD camera in the city, i imported my footage into after effects and polished my clip and added the effecs etc. i then exported (make movie) using the Windows Media - 9player preset. the footage was great, not too large a file and a smooth clip of film.

Okay now here's the problem(s): A day ago i was using after effects to create the effect heavy intro to my filming using animation footage from cinema 4d and various effects/text from AE. I went to export as Windows Media, rendered and watched the footage in confusion. The footage was lacking in resolution, choppy and had a weird hue on some of the colours. Everything i tried did nothing, OpenGL disabled/enabled, changing the quality or bitrate or just re-rendering.
I dont understand as my previous footage was perfect. The only thing i could do was render as a uncompressed AVI and the encode in Adobe Media Encoder as a windows media, but then the file was a little bit choppy.

Help me please?

oh one more thing, when i try to export as Quicktime, my quicktime player says a 'component is missing', could anybody help?
Thank you - Adam