I had this problem on several versions, but most recently with
Version 1.0.2.2413
After the server was running for a while, this process would go to 100% and stay there
/usr/lib/plexmediaserver/Plex Media Scanner --analyze --item 66,41,75,14957,9640,69,58,10136,81,57 --log-file-suffix Analysis
Looking at the logs, it was always one file that was being analyzed
10 Sunny.m4a
that I have copied here
https://drive.google.com/file/d/0BxoVfJq3P2-bLXg0X0c5aW4tM1U/view?usp=sharing
I'm attaching the Analysis log which has a bunch of messages from ffmpeg
I removed the file and everything is normal now so I'm quite certain it's this file.