Ya he encontrado la solucion, por si a alguno le pasa lo que hay que hacer es
1) Open TMPGEnc and press Cancel if Wizard pops up
2) Go to Option->Environmental Setting...->VFAPI plug-in
3) Adjust the plug-in priorities (this is done by right clicking on
the plug-in and choosing Higher priority as many times as
necessary) to match the following:
DirectShow Multimedia File Reader.......3
AVI2(OpenDML) File Reader................1
AVI VFW compatibility Reader.............0
CyberLink MPEG-2 Decoder.................0
Microsoft MPEG-1 Decoder.................0
Wave File Reader..............................0
BMP/PPM/TGA/JPG File Reader...........-2
DVD2AVI Project File Reader 1.76+.....-2*
TMPGEnc Project File Reader 2.58......-2*
4) Press OK
5) Now you can load your XviD AVI into TMPGEnc just like any other
AVI and encode as you wish