Hi Ucom,
it looks like a 100% cpu utilization issue, you need to setup master port to enable the switch chip to do wire speed switching. To do that just select ether2 port as the master which will act as Layer 3 and set all the others (client 1, client2, fileserver) as slave then test the stuff again and throughput of both clients will be only dependent on fileserver performances.
Look here for examples http://wiki.mikrotik.com/wiki/Manual:Switch_Chip_Features
Setting a master port won’t help, as he is doing layer 3 routing and not layer 2 switching. Also, only the CCR1009 has a switch chip. (the OP didn’t specify the model)
Ucom - I’ve seen this same issue with my CCR1016, It ended up being my Mangle rules. Also make sure you aren’t NAT’ing between the two subnets, that will slow it down too. Unfortunately, RouterOS 6 doesn’t fully support the multi-core processors. Routing, NAT and Mangle are all single thread processes, so once you max out that core, it’s done.
The OP is doing a mix of switching and routing, he has 2 networks running on the same L2 broadcast domain (eth2 has ip addresses from 2 different networks) plus client 1 to fileserver connection is around wirespeed, this is why I assumed he uses CCR1009 and I told him to use the switch chip also for client 2.
@Ucom: Can you please post the output of /export hide-sensitive so we can check where is your bottleneck?