<<Was busy writing this when you posted, will take a look>>
I think I made a breakthrough inspired by your comments, seems you were right, so hopefully this helps.
Was troubleshooting, looking if I can still consistantly recreate etc, and I noticed that I see a difference.
Booting with TrueNAS-13.0-U5.2 I get 1x bridge, but booting with TrueNAS-13.0-U5.3 I have 2x bridge!!
So with I TrueNAS-13.0-U5.2 get bridge0 with all jails members, but with TrueNAS-13.0-U5.3 both bridge0 and bridge1 and the jails spread accross both with some missing even though they are UP.
TrueNAS-13.0-U5.2 Boot
Code:
igb0: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=4a520b9<RXCSUM,VLAN_MTU,VLAN_HWTAGGING,JUMBO_MTU,VLAN_HWCSUM,WOL_MAGIC,VLAN_HWFILTER,VLAN_HWTSO,RXCSUM_IPV6,NOMAP>
ether 70:85:c2:db:2c:84
inet 10.0.0.5 netmask 0xffffff00 broadcast 10.0.0.255
media: Ethernet autoselect (1000baseT <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
lo0: flags=8049<UP,LOOPBACK,RUNNING,MULTICAST> metric 0 mtu 16384
options=680003<RXCSUM,TXCSUM,LINKSTATE,RXCSUM_IPV6,TXCSUM_IPV6>
inet6 ::1 prefixlen 128
inet6 fe80::1%lo0 prefixlen 64 scopeid 0x2
inet 127.0.0.1 netmask 0xff000000
groups: lo
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
pflog0: flags=0<> metric 0 mtu 33160
groups: pflog
wg0: flags=80c1<UP,RUNNING,NOARP,MULTICAST> metric 0 mtu 1420
options=80000<LINKSTATE>
inet 192.168.0.1 netmask 0xffffffff
groups: wg
nd6 options=109<PERFORMNUD,IFDISABLED,NO_DAD>
bridge0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
ether 58:9c:fc:10:d5:45
id 00:00:00:00:00:00 priority 32768 hellotime 2 fwddelay 15
maxage 20 holdcnt 6 proto rstp maxaddr 2000 timeout 1200
root id 00:00:00:00:00:00 priority 32768 ifcost 0 port 0
member: vnet0.5 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 11 priority 128 path cost 2000
member: vnet0.4 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 10 priority 128 path cost 2000
member: vnet0.3 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 9 priority 128 path cost 2000
member: vnet0.2 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 8 priority 128 path cost 2000
member: vnet0 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 7 priority 128 path cost 2000000
member: vnet0.1 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 6 priority 128 path cost 2000
member: igb0 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 1 priority 128 path cost 20000
groups: bridge
nd6 options=9<PERFORMNUD,IFDISABLED>
vnet0.1: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
description: associated with jail: dns as nic: epair0b
options=8<VLAN_MTU>
ether 02:ff:60:fd:33:60
hwaddr 02:4c:0c:f0:98:0a
groups: epair
media: Ethernet 10Gbase-T (10Gbase-T <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
vnet0: flags=8943<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=80000<LINKSTATE>
ether fe:a0:98:67:b0:3f
hwaddr 58:9c:fc:10:ff:93
groups: tap
media: Ethernet autoselect
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
Opened by PID 2024
vnet0.2: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
description: associated with jail: mail as nic: epair0b
options=8<VLAN_MTU>
ether 02:ff:60:65:29:a8
hwaddr 02:a3:60:29:60:0a
groups: epair
media: Ethernet 10Gbase-T (10Gbase-T <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
vnet0.3: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
description: associated with jail: plex as nic: epair0b
options=8<VLAN_MTU>
ether 72:85:c2:14:fa:09
hwaddr 02:9a:40:3c:15:0a
groups: epair
media: Ethernet 10Gbase-T (10Gbase-T <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
vnet0.4: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
description: associated with jail: choke as nic: epair0b
options=8<VLAN_MTU>
ether 02:ff:60:66:11:d0
hwaddr 02:2f:76:a5:e1:0a
groups: epair
media: Ethernet 10Gbase-T (10Gbase-T <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
vnet0.5: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
description: associated with jail: tools as nic: epair0b
options=8<VLAN_MTU>
ether 02:ff:60:0f:85:2e
hwaddr 02:c6:69:75:0b:0a
groups: epair
media: Ethernet 10Gbase-T (10Gbase-T <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
TrueNAS-13.0-U5.3 Boot
Code:
igb0: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=4a520b9<RXCSUM,VLAN_MTU,VLAN_HWTAGGING,JUMBO_MTU,VLAN_HWCSUM,WOL_MAGIC,VLAN_HWFILTER,VLAN_HWTSO,RXCSUM_IPV6,NOMAP>
ether 70:85:c2:db:2c:84
inet 10.0.0.5 netmask 0xffffff00 broadcast 10.0.0.255
media: Ethernet autoselect (1000baseT <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
lo0: flags=8049<UP,LOOPBACK,RUNNING,MULTICAST> metric 0 mtu 16384
options=680003<RXCSUM,TXCSUM,LINKSTATE,RXCSUM_IPV6,TXCSUM_IPV6>
inet6 ::1 prefixlen 128
inet6 fe80::1%lo0 prefixlen 64 scopeid 0x2
inet 127.0.0.1 netmask 0xff000000
groups: lo
nd6 options=21<PERFORMNUD,AUTO_LINKLOCAL>
pflog0: flags=0<> metric 0 mtu 33160
groups: pflog
wg0: flags=80c1<UP,RUNNING,NOARP,MULTICAST> metric 0 mtu 1420
options=80000<LINKSTATE>
inet 192.168.0.1 netmask 0xffffffff
groups: wg
nd6 options=109<PERFORMNUD,IFDISABLED,NO_DAD>
bridge0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
ether 58:9c:fc:10:d5:45
id 00:00:00:00:00:00 priority 32768 hellotime 2 fwddelay 15
maxage 20 holdcnt 6 proto rstp maxaddr 2000 timeout 1200
root id 00:00:00:00:00:00 priority 32768 ifcost 0 port 0
member: vnet0.2 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 9 priority 128 path cost 2000
member: vnet0.1 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 6 priority 128 path cost 2000
groups: bridge
nd6 options=9<PERFORMNUD,IFDISABLED>
vnet0.1: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
description: associated with jail: dns as nic: epair0b
options=8<VLAN_MTU>
ether 02:ff:60:fd:33:60
hwaddr 02:4c:0c:f0:98:0a
groups: epair
media: Ethernet 10Gbase-T (10Gbase-T <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
bridge1: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
ether 58:9c:fc:10:eb:76
id 00:00:00:00:00:00 priority 32768 hellotime 2 fwddelay 15
maxage 20 holdcnt 6 proto rstp maxaddr 2000 timeout 1200
root id 00:00:00:00:00:00 priority 32768 ifcost 0 port 0
member: vnet0 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 7 priority 128 path cost 2000000
member: igb0 flags=143<LEARNING,DISCOVER,AUTOEDGE,AUTOPTP>
ifmaxaddr 0 port 1 priority 128 path cost 20000
groups: bridge
nd6 options=9<PERFORMNUD,IFDISABLED>
vnet0: flags=8943<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
options=80000<LINKSTATE>
ether fe:a0:98:67:b0:3f
hwaddr 58:9c:fc:10:ff:93
groups: tap
media: Ethernet autoselect
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>
Opened by PID 2024
vnet0.2: flags=8963<UP,BROADCAST,RUNNING,PROMISC,SIMPLEX,MULTICAST> metric 0 mtu 1500
description: associated with jail: mail as nic: epair0b
options=8<VLAN_MTU>
ether 02:ff:60:65:29:a8
hwaddr 02:9a:40:3c:15:0a
groups: epair
media: Ethernet 10Gbase-T (10Gbase-T <full-duplex>)
status: active
nd6 options=9<PERFORMNUD,IFDISABLED>