Loris (& the list), did you get this sorted? It seems that I am running into the same problem now. What seems to be happening is that the LaTeX file is created in /tmp/babel-XXXXXX/latex-YYYYYY.tex but the log, aux, etc. files are being created in the current directory (where the file with the LaTeX src block is). Although the PDF file is created properly, it is not where org would expect it to be (maybe)? The LaTeX file in /tmp/ compiles perfectly fine when I compile it manually. Attached is /tmp/ecm.org and here is a screenshot of my /tmp directory: