Jonz,
We're going to need more details in order to help you. Please answer:
- What version of calibre are you using?
- On what operating system (Windows, Linux, Mac) and version?
- The ebooks you're talking about, did they start as PDFs or were they a different format?
- What device are you writing to? Is it your Samsung phone or something else?
- You mention a "single directory", are you putting all the books in the same directory?
- Can you give us an example of the ebook file names?
- Can you give us the "single directory's" full path?
All of these things will help us to figure out if you have a conversion problem, an OS problem/conflict, a device problem, perhaps a wrong setting, etc.