Motion tracking, 3d letters, and such are pretty advanced things to be doing in AE if you're new. I'd highly recommend taking a few weeks and getting yourself grounded in how AE actually works. Go through these resources: Getting started with After Effects
Yes, there's a lot there, but AE is very complicated (as you're discovering!), so it will take a little while to get oriented. Seriously, don't just jump into it; you will only frustrate yourself.
How did you create the 3d letters? If it was with AE's ray-traced renderer, that's the problem. That feature is considered obsolete for a number of reasons - one of which is that it's glacially slow unless you have one of a certain set of GPUs. It's much better to use something like C4D Lite. If you're going to be doing a lot of this kind of thing, Element 3d or Zaxwerks 3d Invigorator would be a good investment. But, again, if you're new to AE, this is not the sort of task with which to start!
First, only the Active Camera renders. If you preview in the Active Camera and the render from the Adobe Media Encoder does not look the same then we need to know all the details of your composition. If everything is set up correctly in the comp the only possible thing I can think of that may cause problems would be if you set the composition to Ray-traced rendering and were relying on your CUDA compatible NVIDIA card to do the rendering. If that is the case I would suggest that you render your comp using the Render Cue and set the output module to the default Lossless unless you need transparency. In that case use the Lossless with Alpha preset but change the Alpha type to Straight alpha.
If none of that helps please give us complete workflow details and a full size screenshot of your comp with all of the modified properties of the layer that is giving you problems revealed. (press the u key twice)