Well, the problem has been solved.
I had a script running that checked the permission of folders and changed them to 770 and a user/group.
The folder the video was from was included in this, so I'm guessing PMS just couldn't access it anymore.
What I did notice though that when another program is running (ex. sabnzbd) pms doesn't take any of the cpu-power anymore. It just stops encoding.
I do have enough power to run both (Amd Phenom II X6 + 8GB ram), but all the pms processes just stop.
One other particular thing is that when playing a .iso it just fast forwards. So when just playing it, it start to fast forward by itself.....
edit: I'm pretty sure the problem of fast forwarding from iso's has something to do with the package.
I tested this on another pc that runs ubuntu 11.04 x64.
With the normal install I can run the iso just fine, with this package not.
So I changed all the settings from your install to the ones I have from the default one, nothing changed.
It may also be due to PMS itself, the default is 1.50.0.
Here is a debug.log, maybe you can use it: http://pastebin.com/gyMnU2HJ