Networking :: Very Low Network Performance In Host-to-host Connections

The internal network is behind nat done by the PC Router.The TP Link is recieving wireless signal from outdoors and it has switching and basic routing capabilities. I'm using the PC router for better routing options.PC Router (or R for short) is a triple-booting machine - Linux, FreeBSD and Windows. It has two lan cards - external (ext_if) - 100Mbps Realtek 8139 and internal (int_if) - 1Gbps integrated Realtek 8169.The problem is that all traffic from R to the network is slow - about 5-20K, while the traffic in the oppoiste direction is all right - about 10MB that is fine for 100Mbps cables, NICs and switches. The problem persist no matter the OS the pc R is running.I've tried some debugging on the situation as follows:

- put another PC at the place of R - everything is fine. That exclude the possibility of damaged cables, RJ-45s, switches and etc.
- connected both of the NICs to the Internet while the internal network is being disconnected and they both work fine (no delays)
- traffic shaping is not running
- there is nothing in firewalls except NATing the internal network (and it is working fine). Actually these firewall rules have been operational for more than months and everything was fine untill a week or two ago.
- changed the internal NIC with another
- connected the internal network directly to the TP and all of the PCs are getting good network performance. Then connected the R machine to the TP as well and there was good performance between the internal network PCs and R.
- R has good performance to the TP. In fact everything has good performance directly to the TP (when not connecting trough R).
- the problem persist only between R and machines from the internal network.