They are exactly the same, but mencoder that they use might not be the same. Media Converter is supposed to use half fps (for 352 resolutions) if it's able to detect the source video fps, but 15 fps if not. Apparently this halving *should* give more reliable audio sync than using 15 fps. I haven't had the luxury of being able to investigate it further. Comments on this subject are very welcome.
LINUX Execution conversion with: mencoder "/home/igor/video/11.avi" -oac mp3lame -lameopts abr:br=64 -ovc lavc -lavcopts vcodec=mpeg4:dark_mask=0.2:aspect=15/9:keyint=250:vbitrate=512:trell=yes:v4mv=yes:vpass =1 -vf crop=0:0,scale=352:288 -idx -ffourcc DIVX -ofps 15 -endpos 00:00:30 -o /home/igor/video/770/11.avi WINDOWS Execution conversion with: mencoder.exe "D:/My Documents/My Videos/11.avi" -oac mp3lame -lameopts abr:br=64 -ovc lavc -lavcopts vcodec=mpeg4:dark_mask=0.2:aspect=15/9:keyint=250:vbitrate=512:trell=yes:v4mv=yes:vpass =1 -vf crop=613:368,scale=352:288,eq2=1.0:1.2:0.0:1.7 -idx -ffourcc DIVX -ofps 11.99 -endpos 00:00:30 -o "D:/My Documents/My Videos/770/11.avi"