I've ran into this before, but I guess I wasn't able to clearly explain what the issue was at the time... so let's try again.
I'm exporting an Org file in UTF-8 to LaTeX. Unless I switch the coding system in Emacs from "default" to "UTF-8" (which has the side effect that any new buffer will have UTF-8 coding, which is usually not what I want), the LaTeX buffer gets created with ISO8859-1/latin-1 encoding (which is dead wrong, because several characters in the document are in fact not representable in that encoding). Changing the option "Org Export Latex Coding System" to utf-8 doesn't change how the LaTeX buffer gets created, but it will then helpfully ask when its time to save the buffer if I want to save it as UTF-8 (no, I want it created with UTF-8, not changed to a different encoding on save). That salvages a few characters, but the larger damage of \usepackage[latin1]{inputenc} doesn't get changed of course. The coding system of any export buffers should by default follow the Org buffer they are created from and any changes to the coding system stipulated by export configuration must be applied before the buffer coding system gets used to make any decisions on how to export things. Regards, Achim.