Successfully recompiled ffmpeg again under the mingw environment. The options used are
--extra-cflags=-I/usr/local/ffmpeg/include --extra-ldflags=-L/usr/local/ffmpeg/lib --enable-libmp3lame --enable-libfaac --enable-libfaad --enable-amr-nb --enable-amr-wb --disable-ffserver --disable-ffplay --enable-memalign-hack --enable-gpl --enable-xvid --enable-x264 --enable-libdts --enable-liba52 --enable-w32threads
Major changes are that this version is using faac-1.25.tar.gz, faad2-2.5.tar.gz. Also the AMR codes are no longer embedded into the ffmpeg source codes. They needs to be compiled as separate library before compiling ffmpeg.