I noticed that if I run make clean twice in the gst-ffmpeg code some error messages are generated in the second make clean. 

A new autogen run is required to be able compile the code again.

Example of the error messages:

cd ffmpeg && make distclean
make[4]: Entering directory `/home/jep/cvs/gst-ffmpeg/gst-libs/ext/ffmpeg'
Makefile:5: config.mak: No such file or directory
cc -I -I -I/libavutil -I/libavcodec -I/libavformat -I/libswscale -I/libavdevice -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_ISOC9X_SOURCE -DHAVE_AV_CONFIG_H  -MM vhook/fish.c vhook/null.c vhook/watermark.c vhook/drawtext.c vhook/imlib2.c vhook/ppm.c | sed 's,^\([a-z]\),vhook/\1,' > .vhookdep
vhook/fish.c:47:23: error: framehook.h: No such file or directory
vhook/fish.c:48:21: error: dsputil.h: No such file or directory
vhook/fish.c:49:22: error: avformat.h: No such file or directory
vhook/fish.c:50:21: error: swscale.h: No such file or directory
vhook/null.c:23:23: error: framehook.h: No such file or directory
vhook/null.c:24:21: error: swscale.h: No such file or directory
vhook/watermark.c:61:20: error: common.h: No such file or directory
vhook/watermark.c:62:22: error: avformat.h: No such file or directory
vhook/watermark.c:64:23: error: framehook.h: No such file or directory
vhook/watermark.c:65:22: error: cmdutils.h: No such file or directory
vhook/watermark.c:66:21: error: swscale.h: No such file or directory
vhook/drawtext.c:48:23: error: framehook.h: No such file or directory
vhook/drawtext.c:61:10: error: #include espera "NOM_DE_FITXER" o <NOM_DE_FITXER>
vhook/drawtext.c:62:10: error: #include espera "NOM_DE_FITXER" o <NOM_DE_FITXER>
vhook/imlib2.c:48:23: error: framehook.h: No such file or directory
vhook/imlib2.c:49:21: error: swscale.h: No such file or directory
vhook/imlib2.c:61:18: error: eval.h: No such file or directory
vhook/ppm.c:28:23: error: framehook.h: No such file or directory
vhook/ppm.c:29:22: error: avformat.h: No such file or directory
vhook/ppm.c:30:21: error: swscale.h: No such file or directory
vhook/ppm.c:31:22: error: avstring.h: No such file or directory
/version.sh 
make[4]: /version.sh: Command not found
make[4]: *** No rule to make target `config.mak'.  Stop.
make[4]: Leaving directory `/home/jep/cvs/gst-ffmpeg/gst-libs/ext/ffmpeg'
make[3]: *** [clean-local] Error 2
make[3]: Leaving directory `/home/jep/cvs/gst-ffmpeg/gst-libs/ext'
make[2]: *** [clean-recursive] Error 1
make[2]: Leaving directory `/home/jep/cvs/gst-ffmpeg/gst-libs/ext'
make[1]: *** [clean-recursive] Error 1
make[1]: Leaving directory `/home/jep/cvs/gst-ffmpeg/gst-libs'
make: *** [clean-recursive] Error 1