Could you post the script you use?
I have a script in $HOME/bin/ that uses mencoder. If I hadn't used the third line, I would see two extensions as well. I suspect you are not removing the extension from the input file, and tacking on .mp4 after the -o option.
if [ -f "$videoin" ]; then
mencoder -vf scale=480:272 -ofps 29.97 -ffourcc XVID \
-oac mp3lame -lameopts cbr:br=128 \
-ovc xvid \
-xvidencopts max_bframes=0:quant_type=mpeg:bitrate=1024 \
-af resample=44100 \