Oh, thanks. Didn't notice my typo!
Solved......

Running in CLI with the following params from uTorrent: filebot -script fn:amc --output "F:/media" --action copy --conflict override -non-strict -no-xattr --def plex=xxx.xxx.xxx.xxx subtitles=en,nb,da,sv sclean=y "seriesFormat=Z:/{n}/{episode.special ? \"Special\" : \"Season \"+s.pad(2)}/{n ...

Windows Server 2008 R2
Mounted disks as NFS-shares (It may have to do with that??) over network
EXT4 partition scheme on the drives where it's located.

EDIT:
I will try SMB instead.

EDIT 3:
It's back again, how do I solve this?

Hello, I modified the output by using arguments. Now it it doesn't clean up metadata after the files it moved. Here is the log file http://pastebin.com/Ppfm9w8r My parameters: filebot -script fn:amc --output "F:/media" --log-file amc.log --action copy --conflict override -non-strict --def clean=y ...