It shows you in the log file not in the log window.
First you have to check "Log all tool output" on bottom left corner.
Then open log.txt which is created in the same directory you have XenonMKV.
Your looking for something in log.txt that looks something like this:
[3/7/2010 12:19 PM] [W]C:\Users\Will\Desktop\XboX\XenonMKV\tools\mp4box\MP4Box_default.exe "D:\XBOX\output.mp4" -add video.h264 -fps 24.24 -par 1=1:1 -add audio.m4a -tmp "D:\XBOX" -itags name="The.Cove.2009.PROPER.1080p.BluRay.x264-CiNEFiLE-1"
[3/7/2010 12:19 PM] [W]Generating MP4 file from x264 video and 2-channel AAC.
[3/7/2010 12:19 PM] [W]Using mp4box version 0.4.6-dev (default, February 2009) to generate file.
See the -fps in red? See how it says 24.24? That should be 24.000. So I had to manually run MP4BOX to create the file using the correct FPS.
Meaning, I simply had to open a cmd window and ran:
C:\Users\Will\Desktop\XboX\XenonMKV\tools\mp4box\MP4Box_default.exe "D:\XBOX\output.mp4" -add D:\XBOX\video.h264 -fps 24.000 -par 1=1:1 -add D:\XBOX\audio.m4a -tmp "D:\XBOX" -itags name="The.Cove.2009.PROPER.1080p.BluRay.x264-CiNEFiLE-1"
So all I changed was fps and added the full path to video.h264 and audio.m4a .
NOTE: Make sure Tools > Delete Temporary Files is not enabled.
Of course if the original file is over 4096MB then you will need to do this for all parts that XenonMKV created.
BTW you really should update the MKVToolnix files that come with XenonMKV from:
http://www.bunkus.org/videotools/mkvtoolnix/Lot's of bugs have been fixed since version 2.9.7 that you're using.
Just download the installer and let it install. Then go to the directory it installed the files to and copy them all to your XenonMKV, over-ridding the old ones.