I recently downloaded the newest version to install on my intrepid laptop using the build wizard. All went (hopefully) well and after fiddling with it for a while I went to go render to ogg and some of the codecs were missing. I searched and found in the FAQ and common troubleshooting guide that I needed the proper packages installed, but when I looked they were already there.

I know I have the right codecs, and am pretty sure I enabled these in the ffmpeg configuration of the build wizard. (see screenshot). Any suggestions?

bump - I looked in the FAQ and found out some of the codecs needed had broken dependencies; I fixed the broken ones and that fixed the libmp3lame problem. Now it still complains about ogg/theora.

Did you install libtheora-dev and libogg-dev ? Try installing these and then re-compile.