The filebench cvs repository is broken, the file config.h.in is empty :
http://filebench.cvs.sourceforge.net/viewvc/\*checkout*/filebench/filebench/config.h.in?revision=1.8
It's not a big deal because it can be build by the makefile. But you need a good config.h.in to generate the makefile. So the bootstrap is not easy.
Agree, actually the whole auto-tool chain is applied to the legacy Filebench badly. We have rewritten it from scratch in
http://www.fsl.cs.sunysb.edu/~vass/filebench/
Fixed in 1.4.9:
1) We use git repo
2) config, make, make install should work without any problems