Some thoughts (many not related to the problem at hand...)
You don't appear to have much in the way of a functional firewall on this device, I will assume it is for internal use only.
It looks likely running V7 routerOS.
The following should be changed to 30S
/ip firewall connection tracking
set udp-timeout=10s
On this unit.
V7 is much slower at routing than V6,
VLAN filtering functionality is much improved in V7 (has hardware offloading).
(So it works well as a managed L2 switch)
However, you seem to be forcing all the L2 VLAN filtering to be done in software.
Apart from being slow this likely clogs up the CPU/Switch bottleneck unnecessarily.
On the WAN port, you have connected it to a bridge, this is necessary if the WAN interface is receiving
priority tagged packets, but otherwise likely just adds overhead.
There is also Ethernet flow control which can block things, I think its default is off though.
I think a configuration using a hardware offloaded VLAN filtering bridge would be better.
An approximation to yours using vlan filtering.
(I have kept the separate bridge_wan, the eoip tunnels endpoints need fixing)
# 2026-09-26 12:32:09 by RouterOS 7.24.4
#
# model = RB750Gr3
/interface bridge
add admin-mac=74:4D:28:C9:4E:98 auto-mac=no name=bridge-wan port-cost-mode=\
short protocol-mode=none
add name=bridge_lan protocol-mode=none vlan-filtering=yes
/interface ethernet
set [ find default-name=ether1 ] advertise=\
10M-baseT-half,10M-baseT-full,100M-baseT-half,100M-baseT-full
set [ find default-name=ether2 ] advertise="10M-baseT-half,10M-baseT-full,100M\
-baseT-half,100M-baseT-full,1G-baseT-full"
/interface eoip
add mac-address=02:0B:4D:C9:CE:1A name=eoip31 remote-address=172.16.31.31 \
tunnel-id=1031
add mac-address=02:0B:4D:C9:CE:1B name=eoip39 remote-address=172.16.39.39 \
tunnel-id=1039
/interface vlan
add interface=bridge_lan loop-protect=off name=vlan31 vlan-id=1902
add interface=bridge_lan name=vlan39 vlan-id=39
/interface list
add comment=defconf name=WAN
add comment=defconf name=LAN
/interface wireless security-profiles
set [ find default=yes ] supplicant-identity=MikroTik
/ip pool
add name=pool1 ranges=192.168.88.11-192.168.88.99
/ip dhcp-server
add address-pool=pool1 interface=bridge_lan name=server1
/interface bridge port
add bridge=bridge_lan interface=ether3
add bridge=bridge_lan ingress-filtering=no interface=ether4 \
internal-path-cost=10 path-cost=10
add bridge=bridge_lan ingress-filtering=no interface=ether5 \
internal-path-cost=10 path-cost=10
add bridge=bridge-wan hw=no ingress-filtering=no interface=ether1 \
internal-path-cost=10 path-cost=10
add bridge=bridge_lan hw=no ingress-filtering=no interface=ether2 \
internal-path-cost=10 path-cost=10 pvid=39
add bridge=bridge_lan ingress-filtering=no interface=eoip31 \
internal-path-cost=10 path-cost=10 pvid=1902
add bridge=bridge_lan ingress-filtering=no interface=eoip39 \
internal-path-cost=10 path-cost=10 pvid=39
/ip firewall connection tracking
set udp-timeout=30s
/ip neighbor discovery-settings
set discover-interface-list=LAN
/interface bridge vlan
add bridge=bridge_lan tagged=bridge_lan untagged=ether2,eoip39 vlan-ids=39
add bridge=bridge_lan tagged=ether2,bridge_lan untagged=eoip31 vlan-ids=1902
add bridge=bridge_lan untagged=ether3,ether4,ether5,bridge_lan vlan-ids=1
/interface list member
add comment=defconf interface=ether2 list=LAN
add comment=defconf interface=bridge-wan list=WAN
add interface=vlan31 list=LAN
add interface=bridge_lan list=LAN
/ip address
add address=172.17.39.209/24 interface=vlan39 network=172.17.39.0
add address=172.17.31.209/24 interface=vlan31 network=172.17.31.0
add address=192.168.88.1/24 interface=bridge_lan network=192.168.88.0
/ip dhcp-client
add comment=defconf interface=bridge-wan name=bridge-wan
/ip dhcp-server network
add address=192.168.88.0/24 dns-server=192.168.88.1 gateway=192.168.88.1
/ip dns
set allow-remote-requests=yes
/ip dns static
add address=192.168.88.1 name=router.lan type=A
/ip firewall filter
add action=drop chain=input dst-port=53 in-interface=bridge-wan protocol=tcp
add action=drop chain=input dst-port=53 in-interface=bridge-wan protocol=udp
add action=fasttrack-connection chain=forward connection-state=\
established,related
/ip firewall nat
add action=masquerade chain=srcnat out-interface=bridge-wan src-address=\
192.168.88.0/24
/ip ipsec profile
set [ find default=yes ] dpd-interval=2m dpd-maximum-failures=5
/ip service
set ftp disabled=yes
set ssh disabled=yes
set telnet disabled=yes
set www disabled=yes
set reverse-proxy disabled=yes
set api disabled=yes
set api-ssl disabled=yes
/routing bfd configuration
add disabled=no interfaces=all min-rx=200ms min-tx=200ms multiplier=5
/tool graphing interface
add interface=ether1
add interface=vlan31
add interface=eoip39