I think I have discovered the problem(s) and I may not have explained myself correctly the first time:
Say I have a folder structure as follows:
C:\TV\ProgramName S07E05\What's in a name.mkv
Now If I go into C:\TV\ProgramName S01E10 and choose a file, DOPUS renames one file and fails on the second .txt file. I only want it to rename the selected file (in this case the MKV file and not the .txt files). My workaround to this was to add: WHENEXISTS=skip
Another issue is that if I use Flat View from 'C:\TV' and choose 'Mixed (no folders), then select all the *.MKV files then it renames the first file to 'TV' and tries to do the same for all other files and fails. I can kind of see the logic of why it would do this but is there a way around it? Of course it's very plausible that I doing something wrong here!
Thanks once again.