Would be handy if you could paste in the script itself, or at least the variables being used, but I expect I know what the error is or at least one of them...
There are two sets of variable paths, some require backslash (\) the others require forward slash(/)..
The library file paths at least are the wrong way round:
"E:\TV Shows" should be "E:/TV Shows"
However as stated in my recent update, the full script isn't really required, you just need to paste the one line in the first post in to uTorrent (amending your own paths) which will then be much less disk activity.
I've amended below with your details, you should just be able to paste this in to utorrent in the "run this program on completion" field and it should all work
I've changed it to show it's running, so you can change filebot to filebot.launcher.exe if you want it to run hidden.
filebot -script fn:amc --output "C:/Users/Billy/Videos" --log-file amc.log --action copy --conflict override -non-strict --def "ut_dir=%D" "ut_file=%F" "ut_kind=%K" "ut_title=%N" "ut_label=%L" "ut_state=%S" music=N artwork=n plex=localhost deleteAfterExtract=n clean=n excludeList=amc-input.txt "seriesFormat=E:/TV Shows/{n}/{'S'+s}/{fn}" "animeFormat=C:/Users/Billy/Videos/Movies/{n}/{fn}" "movieFormat=C:/Users/Billy/Videos/Movies/{n} {y}/{fn}"