Ok, weired one here guys.

Ok, so what I'm doing is splitting a CRS125-24G into 2 separate routers essentially.
Some ports on VLAN300, some on VLAN400 then one on the "WAN"

All works great, plug into one of the VLAN300 allocated ports and get an IP on that range no worries, plug into the VLAN400 ports, get an IP in that range all great.
Using my windows laptop everything works as expected, I can ping the router on it's local VLAN IP, I can use winbox etc and I can ping through the router to the WAN
This is where it's really weird, when I use my Centos7 laptop or my Centos 6.5 servers I plugin to a VLAN300 or VLAN400 port, I get an IP in that range but then I can NOT communicate with the router in ANY way, I CAN communicate with other machines on that VLAN(My windows laptop)

I've been banging my head against the wall on this one, any help much appreciated.

Hers what I have tested
-Complete rebuild of the config - MUltiple times
-system reset-configuration no-defaults=yes
-Different Linux machines, different NIC's in those machines
-Connecting the Linux machine to a dumb switch then connecting the switch to the MT


Here is my config... help!

I think ive nailed this one myself.
Seems like an obscure Mikrotik issue.

My original config had each of the 3 groups using their own master port, then each VLAN was applied to that master port.

VLAN 200 would always work AOK, but packets form the router coming out of VLAN300 and VLAN400 ports had the VLAN tagging applied still(Seen by wireshark)

I amended my config to use ether2 as the master port for all interfaces then applied all 3 vlan's to ether 2.
This is the post that inspired me - http://forum.mikrotik.com/viewtopic.php?f=2&t=88015

Here is my working config as of right now

ros code

/interface ethernet
set [ find default-name=ether1 ] name=WAN
set [ find default-name=ether5 ] master-port=ether2
set [ find default-name=ether6 ] master-port=ether2
set [ find default-name=ether7 ] master-port=ether2
set [ find default-name=ether8 ] master-port=ether2
set [ find default-name=ether9 ] master-port=ether2
set [ find default-name=ether10 ] master-port=ether2
set [ find default-name=ether11 ] master-port=ether2
set [ find default-name=ether12 ] master-port=ether2
set [ find default-name=ether13 ] master-port=ether2
set [ find default-name=ether14 ] master-port=ether2
set [ find default-name=ether15 ] master-port=ether2
set [ find default-name=ether16 ] master-port=ether2
set [ find default-name=ether17 ] master-port=ether2
set [ find default-name=ether18 ] master-port=ether2
set [ find default-name=ether19 ] master-port=ether2
set [ find default-name=ether20 ] master-port=ether2
set [ find default-name=ether21 ] master-port=ether2
set [ find default-name=ether22 ] master-port=ether2
set [ find default-name=ether23 ] master-port=ether2
set [ find default-name=ether24 ] master-port=ether2
/interface vlan
add interface=ether2 l2mtu=1584 name=VL200 vlan-id=200
add interface=ether2 l2mtu=1584 name=VL300 vlan-id=300
add interface=ether2 l2mtu=1584 name=VL400 vlan-id=400
/ip pool
add name=vlan200 ranges=192.168.20.50-192.168.20.90
add name=vlan300 ranges=192.168.30.60-192.168.30.90
add name=vlan400 ranges=192.168.40.90-192.168.40.150
/ip dhcp-server
add address-pool=vlan400 disabled=no interface=VL400 name=server3
add address-pool=vlan300 disabled=no interface=VL300 name=server2
add address-pool=vlan200 disabled=no interface=VL200 name=server1
/port
set 0 name=serial0
/interface ethernet switch egress-vlan-tag
add tagged-ports=switch1-cpu vlan-id=200
add tagged-ports=switch1-cpu vlan-id=300
add tagged-ports=switch1-cpu vlan-id=400
/interface ethernet switch ingress-vlan-translation
add customer-vid=0 new-customer-vid=200 ports=ether5 sa-learning=yes
add customer-vid=0 new-customer-vid=200 ports=ether6 sa-learning=yes
add customer-vid=0 new-customer-vid=200 ports=ether7 sa-learning=yes
add customer-vid=0 new-customer-vid=200 ports=ether8 sa-learning=yes
add customer-vid=0 new-customer-vid=200 ports=ether9 sa-learning=yes
add customer-vid=0 new-customer-vid=200 ports=ether10 sa-learning=yes
add customer-vid=0 new-customer-vid=300 ports=ether11 sa-learning=yes
add customer-vid=0 new-customer-vid=300 ports=ether12 sa-learning=yes
add customer-vid=0 new-customer-vid=300 ports=ether13 sa-learning=yes
add customer-vid=0 new-customer-vid=300 ports=ether14 sa-learning=yes
add customer-vid=0 new-customer-vid=300 ports=ether15 sa-learning=yes
add customer-vid=0 new-customer-vid=300 ports=ether16 sa-learning=yes
add customer-vid=0 new-customer-vid=400 ports=ether17 sa-learning=yes
add customer-vid=0 new-customer-vid=400 ports=ether18 sa-learning=yes
add customer-vid=0 new-customer-vid=400 ports=ether19 sa-learning=yes
add customer-vid=0 new-customer-vid=400 ports=ether20 sa-learning=yes
add customer-vid=0 new-customer-vid=400 ports=ether21 sa-learning=yes
add customer-vid=0 new-customer-vid=400 ports=ether22 sa-learning=yes
add customer-vid=0 new-customer-vid=400 ports=ether23 sa-learning=yes
add customer-vid=0 new-customer-vid=400 ports=ether24 sa-learning=yes
/interface ethernet switch vlan
add ports=ether17,ether18,ether19,ether20,ether21,ether22,ether23,ether24,switch1-cpu vlan-id=400
add ports=ether5,ether6,ether7,ether8,ether9,ether10,switch1-cpu vlan-id=200
add ports=ether11,ether12,ether13,ether14,ether15,ether16,switch1-cpu vlan-id=300
/ip address
add address=192.168.40.1/24 interface=VL400 network=192.168.40.0
add address=192.168.30.1/24 interface=VL300 network=192.168.30.0
add address=192.168.20.1/24 interface=VL200 network=192.168.20.0