@Yama4050242: please have a look at my generic problem reporting guidelines:
http://forum.doom9.org/showthread.php?t=96137
As it is now I have to ask you a dozen questions to get an idea about what you're doing. I kindly ask that you do provide all that info without me having to ask for it. AS a general rule, if you tell people everything you do since the start of the program in question, it makes things much easier. For instance, MeGUI supports 4 codecs.. since you have an MP3 I know it's not Snow but that still leaves 3 other possibilities, plus two different encoders for x264. Then, there's a manual mode, a manual mode in which multiple jobs are generated, and an automated mode. That alone gives us 4 * 3 = 12 permutations not taking into account any settings you may have changed, or how you determine that the output has the wrong framerate. I also don't see a logfile.. for instance if there was a problem detecting the framerate, the log would possibly reflect upon that.