This time it was running on 6.42.3 (both firmware and routeros).
Soft reboot of helped.
/interface bridge
add admin-mac=64:D1:54:11:B0:7C auto-mac=no comment="created from master port" name=bridge1 protocol-mode=none
/interface ethernet
set [ find default-name=ether1 ] comment="Master interface VLAN switchu pre pristup na CPU" loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether2 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether3 ] comment="tnet1, tnet2, tnet3" loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether4 ] comment="tnet1, tnet2, tnet3 backup" loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether5 ] comment=tnet4 loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether6 ] comment="tnet4 backup" loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether7 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether8 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether9 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether10 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether11 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether12 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether13 ] comment=center loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether14 ] comment=center-backup loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether15 ] comment=jmi-backup loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether16 ] comment=jmi loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether17 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether18 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether19 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether20 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether21 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether22 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether23 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=ether24 ] loop-protect=on loop-protect-send-interval=10s
set [ find default-name=sfp1 ] disabled=yes
/interface vlan
add interface=bridge1 name=vlan-jmi vlan-id=6
/interface ethernet switch
set drop-if-invalid-or-src-port-not-member-of-vlan-on-ports=\
ether1,ether2,ether3,ether4,ether5,ether6,ether7,ether8,ether9,ether10,ether11,ether12,ether13,ether14,ether15,ether16,ether17,ether18,ether19,ether20,ether21,ether22,ether23,ether24,sfp1,switch1-cpu forward-unknown-vlan=no \
unknown-vlan-lookup-mode=ivl
/interface wireless security-profiles
set [ find default=yes ] supplicant-identity=MikroTik
add authentication-types=wpa2-psk eap-methods="" management-protection=allowed mode=dynamic-keys name=xmi supplicant-identity="" wpa2-pre-shared-key=xxxxxxxxx
/interface wireless
set [ find default-name=wlan1 ] band=2ghz-b/g/n frequency=2442 frequency-mode=superchannel mode=ap-bridge security-profile=xmi ssid=xmi2 tx-power=22 tx-power-mode=all-rates-fixed wireless-protocol=802.11
/snmp community
set [ find default=yes ] addresses=0.0.0.0/0
/interface bridge port
add bridge=bridge1 interface=ether2
add bridge=bridge1 interface=ether3
add bridge=bridge1 interface=ether4
add bridge=bridge1 interface=ether5
add bridge=bridge1 interface=ether6
add bridge=bridge1 interface=ether7
add bridge=bridge1 interface=ether8
add bridge=bridge1 interface=ether9
add bridge=bridge1 interface=ether10
add bridge=bridge1 interface=ether11
add bridge=bridge1 interface=ether12
add bridge=bridge1 interface=ether13
add bridge=bridge1 interface=ether14
add bridge=bridge1 interface=ether15
add bridge=bridge1 interface=ether16
add bridge=bridge1 interface=ether17
add bridge=bridge1 interface=ether18
add bridge=bridge1 interface=ether19
add bridge=bridge1 interface=ether20
add bridge=bridge1 interface=ether21
add bridge=bridge1 interface=ether22
add bridge=bridge1 interface=ether23
add bridge=bridge1 interface=ether24
add bridge=bridge1 interface=sfp1
add bridge=bridge1 interface=ether1
/interface ethernet switch egress-vlan-tag
add vlan-id=1
add tagged-ports=ether13,ether14,switch1-cpu vlan-id=6
add tagged-ports=ether3,ether4,ether13,ether14 vlan-id=11
add tagged-ports=ether3,ether4,ether13,ether14 vlan-id=12
add tagged-ports=ether3,ether4,ether13,ether14 vlan-id=13
add tagged-ports=ether3,ether4,ether5,ether6,ether13,ether14 vlan-id=99
add tagged-ports=ether5,ether6,ether13,ether14 vlan-id=50
add tagged-ports=ether13,ether14 vlan-id=999
add tagged-ports=ether13,ether14 vlan-id=132
add tagged-ports=ether13,ether14 vlan-id=89
add tagged-ports=ether11,ether12,ether13,ether14 vlan-id=30
add tagged-ports=ether11,ether12,ether13,ether14 vlan-id=69
add tagged-ports=ether13,ether14 vlan-id=82
add tagged-ports=ether13,ether14 vlan-id=15
/interface ethernet switch ingress-vlan-translation
add customer-vid=0 new-customer-vid=999 ports=ether1,ether2
add customer-vid=0 new-customer-vid=132 ports=ether7,ether8
add customer-vid=0 new-customer-vid=89 ports=ether9,ether10
add customer-vid=0 new-customer-vid=82 ports=ether11,ether12
add customer-vid=0 new-customer-vid=1 ports=ether13,ether14
add customer-vid=0 new-customer-vid=6 ports=ether15,ether16
add customer-vid=0 new-customer-vid=1 ports=ether19,ether20,ether21,ether22,ether23,ether24
add customer-vid=0 new-customer-vid=1 ports=switch1-cpu
add new-customer-vid=1 ports=sfp1
add customer-vid=0 new-customer-vid=15 ports=ether17,ether18
/interface ethernet switch vlan
add comment=xmi ports=ether13,ether14,ether19,ether20,ether21,ether22,ether23,ether24,sfp1,switch1-cpu vlan-id=1
add comment=jmi ports=ether13,ether14,ether15,ether16,switch1-cpu vlan-id=6
add comment=tnet1 ports=ether3,ether4,ether13,ether14 vlan-id=11
add comment=tnet2 ports=ether3,ether4,ether13,ether14 vlan-id=12
add comment=tnet3 ports=ether3,ether4,ether13,ether14 vlan-id=13
add comment=management ports=ether3,ether4,ether5,ether6,ether13,ether14 vlan-id=99
add comment="horny koniec (cez santika)" ports=ether11,ether12,ether13,ether14 vlan-id=30
add comment="kubo(tommy) (cez kabel od joka)" ports=ether11,ether12,ether13,ether14 vlan-id=69
add comment=kabel-santik-joko-marianSabo ports=ether11,ether12,ether13,ether14 vlan-id=82
add comment=stankovce ports=ether9,ether10,ether13,ether14 vlan-id=89
add comment=vbnet ports=ether7,ether8,ether13,ether14 vlan-id=132
add comment=tnet4 ports=ether5,ether6,ether13,ether14 vlan-id=50
add comment="internet (slovanet)" ports=ether1,ether2,ether13,ether14 vlan-id=999
add comment=tnet5 ports=ether13,ether14,ether17,ether18 vlan-id=15
/ip address
add address=192.168.3.10/24 interface=bridge1 network=192.168.3.0
add address=192.168.6.100/24 interface=vlan-jmi network=192.168.6.0
/ip route
add distance=1 gateway=192.168.3.20
/ip service
set telnet disabled=yes
set ftp disabled=yes
set www disabled=yes
/lcd
set default-screen=stats-all read-only-mode=yes
/lcd interface
add interface=bridge1
/lcd interface pages
set 2 interfaces=ether24,sfp1
/system clock
set time-zone-name=Europe/Bratislava
/system identity
set name=Tnet-CoreSwitch
/system ntp client
set enabled=yes primary-ntp=192.168.2.15
/system routerboard settings
set silent-boot=no