Johan - It's perhaps more practical to move away from .fme files and instead use .fmw files instead if you can. As far as I am aware .fme file support is really to maintain backwards compatibility, the main downside to them is that once you save a .fme file you can't then reopen the file in Workbench.
.fmw files can still be run in a batch file with a cmd line like:
fme c:\\temp\\test.fmw
...and they are still associated with the FME Engine.
Sorry I just realised I have of course assumed that you authored your process with Workbench in the first place. Is that the case or have you hand crafted the .fme file?
Today I realized that my problem wasn´t FME 2013- It was just a bad path!
But I will start using .fmw files in my batch files instead - seems easier.
Thanks!
