Take a look at this post:
http://xenonmkv.ev98.net/forum/index.php/topic,162.0.htmlI'm thinking the awfully long file names for the videos you want to convert may be the problem.
MP4Box does NOT like excessively long filenames and this
D:\[AHQ] Fullmetal Alchemist 1-51 [Dual Audio] MKV\[AHQ] Fullmetal Alchemist - 07 - Night Of The Chimera's Cry.mkv
is bordering on the ridiculous.
Try a couple of things:
1. Copy your MKV to a folder with a shorter name or rename your folder to D:\MKV\
2. Rename the file the "Chimera.mkv" (without the quotes, of course)
Even better, move your MKV to the root of your D:\ drive after renaming it, i.e., D:\Chimera.mkv.
Simpifying the MKV full name and converting from the root of the drive has solved MANY an MP4Box problem.