@Malonn: I can't seem to reproduce the problem.
I also did some testing, and I also could not reproduce the issue Malonn reported. In my testing, PyFFI did not care if there were any type of other files in the "in" folder or not, which would agree with the thought that JdeRau stated.
In any case it is a good practice to keep the "in" folder clean of any files one does not want to pyffi.
@Amorilia
I will try out your new release over the weekend and report. Of course, I will retire my two uploads immediately if it works. I got the impression that other users also stumbled, so I provided a quick "dirty" fix until you found time to revisit the config files. I'm sure it is very minor thing that needed to be addressed.
The issue I had with the "improved" .ini's were that Pyffi would start the run but abandon it immediately (like after 1 or 2 seconds) and not treat any files. I got the impression it simply did not pick up the correct path to find the mesh files. Re-introducing the paths settings from the earlier version made it work again. I have retained the non-working .ini wordings after I installed the "improved" version of 2.1.3. However if the newest one will work, it's a moot point sending you the old ones. I'll test the new ones and will report later this weekend.
I will also get back to you on the PM. Thanks for your efforts with PyFFI!!