Hey, I recently ran into a similar problem. Apparently there is a glitch when you queue a sequence in media encoder that contains .mkv files (from AVCHD cards or archives) When working with them in premiere initially I got a status bar at the bottom that said “conforming 00000.mkv” which is some sort of pre rendering it does to interpret the footage without having to transcode it. Apparently when you send it out to AME it has to re-conform the footage, but I didn’t notice the status bar in the bottom of the “select a premiere pro sequence” window. After letting that window sit and do its conforming of the clips again, I hit okay to send the sequence into the queue. The sequence is currently outputting normally without errors (it’s really long) and I had been getting the same thing where it would go for a minute or so then come up with an unknown error.
SO long story short, if you’re working with some form of card based footage (not necessarily AVCHD, could be EXCAM or something else too) straight into PrPro without transcoding, try opening the project via Dynamic Link in Media Encoder and once you navigate to the sequence, but BEFORE you add it to the queue, see if there are any progress bars in the bottom right corner of the window that need to do some thinking before you start the encode.
Hope this helps
Ethan Gallo-