I know for a fact that if you disable the STDi/o as well as "use as internal encoder" options your problems with odd-lengths will be gone. I'd also be willing to bet that you'll lose the problem with the popping at the end.
Now is where Tony's theory comes into play. It may be streaming the full contents of the WAV to the encoder. And the non-music data is causing the pop. If you disable the options mentioned, it doesn't do this.
To use LAME externally, you should not select any special options on the MP3 dialog inside the External Encoder tab. You should only delect the path to your encoder and "User Defined" for argument type. Then specify your command line arguments. I identified these (with the exception of the popping) and a few other problems when changing those settings and reported them to Jackie during the beta of 1.81.
Bruno