Not using virtualdub for this but just in case... MP4box should achieve this simply :
Code:
MP4Box.exe -add video.h264:fps=60 -new Output.mp4
Once you have extracted the video stream from the mkv video (using mkvextract for example) just set the desired fps in the command line
Edit :
this command should do too:
MP4Box.exe -add video.h264 -fps 120 -new Output.mp4