I have fme wb which does fanout with gdb. It means that in the end as output sets of data I get few new created gdb. But If I start this fme wb within python script It does not do fanout. Just write data in one gdb. i do not understand where could be a problem?
I tried this on my system and for me it worked and did the fanout whether I started from python or not. Maybe you could check your fanout parameters against mine.
Here is a sample workspace. And here is the code I used in python: import os print os.system("c:/apps/FME2012/fme.exe C:/Stack/none2filegdb.fmw")