I compiled/installed ffmpeg in /usr/local because the installation in /usr (with checkinstall) fails because it tries to overwrite files installed with ffmpeg related packages (libswscale-dev, libavcodec-dev etc.) which are dependencies of some other programs I use. Everything compiles fine but kdenlive first run wizard reports missing avformat module. I used recommended options except --enable-libamrnb and --enable-libamrwb which are reported as unknown by configure script.
This is all on Ubuntu 9.04 and when I compile only with ffmpeg from repo's avformat module is present.
What is baffling is that I have the same setup with ffmpeg in /usr/local on another machine which works (although the ffmpeg is from April this year).
Does anyone have any idea what is going wrong? Should I pass some options to mlt ./configure or is the problem with ffmpeg or possibly even kdenlive?

Thank you, this works.