Now I installed Xubuntu Precise Pangolin in a third partition of the same machine and did a encode with avidemux (same video, same settings). The result is very astonishing:
LMDE/Xfce: 3 frames/sec
Ubuntu Natty: 9 frames/sec
Xubuntu Precise: 15 frames/sec
I think the difference is how the packages are compiled. Debian packages are compiled for i486, Ubuntu packages are compiled for i686.
IMHO this way LMDE has no future.
I will keep Xubuntu Precise and remove the other 2 partitions.