I was batch encoding several files yesterday, and one of the files failed. Adobe Media Encoder provided no details, other than when I hover over the yellow exclamation point error icon, it says: "Error compiling movie. Unknown error." Very insightful.
Today I reprocessed the file same file with the same preset [FLV - Same As Source (Flash 7 and Higher)] and it worked fine. To check for instability on my machine, I actually ran the same job 10 times, and each job succeeded. But the curious thing is, even though I was using the same input file and output preset, I see that the output files vary in size. The output sizes are:
Now I understand that this variation is less than 10kB on a 30MB file, so it's prety small. But I am curious as to why the file size would vary in this way.
I would guess that you are overclocking your cpu and the cooler is not able to make the cpu cool enough and some calculations can go wrong. There are programs that put the cpu in a high load and check if it's running properly as expected. Give them a try.