any place to look at for PCI-express performance issues ?

hi,
during my tests with netmap with 10Gbit cards (82599, dual port),
i notice that a motherboard with an AMD 880G chipset
is performing significantly worse than an intel based one.
In both cases the NIC is mounted on a 16x PCIe slot,
and in both cases the driver reports the use 5Gb/4x per port.

On the intel i reach easily 14.88Mpps, on the AMD the card tops
at 1.8Mpps, and is not CPU limited (changing dev.cpu.0.freq does not change
the throughput).
Disabling flow control does not help (and in any case
the other end of the link is the same), and since
I am using the same picobsd image (based on FreeBSD/i386
head w/ my netmap code) i suspect that the difference in
performance has to do with the PCIe controller.
My netmap code
http://info.iet.unipi.it/~luigi/netmap/
does nothing special on the bus.

Now, the question is, is there any place in FreeBSD sources that
might be related to PCIe performance, e.g. initialising specific
features in one or another northbridge, etc ?

cheers
luigi