In December I moved from my 4 year old i5-750 desktop build to an Intel NUC system with an i5-4200U, mSATA HDD, Intel 5000 HD Graphics, with a 2TB HDD connected via a USB 3 HDD Dock. 

I upload videos to YouTube all the time, and in order to reduce the file size I take the original MOV file created by the digital camera and convert them into AVI using WinFF or MP4 Windows Live Movie Maker 2011. WinFF was no longer a solution on my Intel NUC system as the same file would take 3-4 times longer to convert, so I moved full time to Windows Movie Maker 2012 which 'most' of the time works fine.

However I have found some videos will get partway through the conversion and then fail - playing back the MP4 file the audio and any extra's will play back but the video will just stop. I am now trying to figure out the cause of the issue and struggling. 
My normal process is to move the MOV file from the digital camera's SD card to a folder on the 2TB, I then open Movie Maker, import the file. 90% of the time I don't need to do any editing and so select the built in YouTube option, select my desktop (on the mSATA) and wait for it to convert. I then play back the file to see if it has failed and if not, move to the 2TB Hard Drive and delete the original MOV file.

If the conversion fails, the only option I seem to have is to reshoot the video and go through the process again.
No combination I can come up with of placing the MOV file on another HDD or what HDD the converted file ends up will correct the issue - the file will fail to convert at the same place each time. 

I have had failed converts on 1 minute files and 10 minute files (200MB to 2GB), but at the same time have had success with 1 minute files and 10 minute files -- and everything in between. There seems to be no rhyme or reason for what file will fail.

Anyone got any thoughts?