[CentOS] iptables marking and NAT issue

Hello all,

It appears that, for some reason I have thus far failed to understand when
you use marking in iptables you then run into troubles if you attempt to do
NAT (MAQUERADE).

Let me describe this in more detail.

We are attempting to use a network test environment named ATCD running it
on a CentOS VM under VirtualBox. For more into on ATCD see:

https://github.com/facebook/augmented-traffic-control

The networking inside the VirtualBox environment is private so at some
point before you get out of it you've got to have a NAT router - not
necessarily on the same VM where the ATCD runs - which also is a router.

Be that as it may, ATCD uses a combination of iptables marking and tc to
degrade/control network transmission quality in accordance with your
settings. And it seems to work just fine up until you reach the NATing
router - at which point the transmission drops to very slow if not
non-existent.

An old article here makes a passing reference to a conflict between
iptables marking and MASQ (NAT):

http://tldp.org/HOWTO/Adv-Routing-HOWTO/lartc.netfilter.html

Unfortunately, the link to another text supposedly detailing how to deal
with this is dead.

Has anybody encountered this? Any tips on how to fix this issue?

Thanks.

Boris.