Did some more testing and found some interesting results.

I forgot to mention the reason for extra SSD is so that I could set up a
dual boot with Windows 10 via GRUB. I have discovered it is Windows that
is creating my problem.

If I boot straight into Linux from power off I have no latency issues.
However if I first boot into Windows, then restart into Linux the
latency issue occurs.

It is definitely related to ASPM as the Linux kernel pcie_aspm=off flag
prevents the issue.

I also tested a bunch of settings in the BIOS and the results (NOK means issue 
still occured):
Boot -> Fast Boot -> Disabled - NOK
Advanced -> Platform Misc Configuration -> PCI Express Native Power Management 
-> Disabled - OK
Advanced -> Platform Misc Configuration -> Native ASPM -> Disabled - OK
Advanced -> PCH Configuration -> ASPM Support -> Disabled - OK
Advanced -> PCH Configuration -> ASPM Support -> Auto - NOK
Advanced -> PCH Configuration -> ASPM Support -> L0s - OK
Advanced -> PCH Configuration -> ASPM Support -> L1 - NOK
Advanced -> PCH Configuration -> ASPM Support -> L0sL1 - OK

I don't really understand much about ASPM and how OSes and BIOSes
control it, but it seems with ASPM support set to auto or L1, then
somehow after the system reboots from Windows some sort of state is left
set which causes the latency. Possibly related to the L1 state.

Anyway I am going to leave ASPM in BIOS set to L0sL1 so that ASPM is
still used but whatever Windows is doing is reset by the BIOS.

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You received this bug notification because you are a member of Kernel
Packages, which is subscribed to linux in Ubuntu.
https://bugs.launchpad.net/bugs/1880076

Title:
  ubuntu 20.4 - retransmitts with r8169

Status in linux package in Ubuntu:
  Expired

Bug description:
  Hi,

  i run some network-tests (iperf3) and noticed massive retransmitts in
  ubuntu 20.4 with kernel 5.4.0-29. I'm using module r8169 for network-
  adapter

  03:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd.
  RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller (rev 15)

  if i boot my ubuntu 18.4 and did same iperf-test (same hardware, same
  network configuration, other client is not rebooted) i have not these
  retransmitts.

  root@bpi-r2:~# iperf3 -c 192.168.0.21                                         
  
  Connecting to host 192.168.0.21, port 5201                                    
  
  [  5] local 192.168.0.11 port 35702 connected to 192.168.0.21 port 5201       
  
  [ ID] Interval           Transfer     Bitrate         Retr  Cwnd              
  
  [  5]   0.00-1.00   sec  14.2 MBytes   119 Mbits/sec  337   14.1 KBytes       
  
  [  5]   1.00-2.00   sec  14.9 MBytes   125 Mbits/sec  331   14.1 KBytes       
  
  [  5]   2.00-3.00   sec  15.1 MBytes   126 Mbits/sec  296   19.8 KBytes       
  
  [  5]   3.00-4.00   sec  14.7 MBytes   124 Mbits/sec  314   14.1 KBytes       
  
  [  5]   4.00-5.00   sec  12.8 MBytes   107 Mbits/sec  259   14.1 KBytes       
  
  [  5]   5.00-6.01   sec  67.4 MBytes   560 Mbits/sec  137    362 KBytes       
  
  [  5]   6.01-7.00   sec   111 MBytes   940 Mbits/sec    0    366 KBytes       
  
  [  5]   7.00-8.00   sec   112 MBytes   941 Mbits/sec    0    409 KBytes       
  
  [  5]   8.00-9.00   sec   112 MBytes   940 Mbits/sec    0    421 KBytes       
  
  [  5]   9.00-10.00  sec   112 MBytes   936 Mbits/sec    0    426 KBytes       
  
  - - - - - - - - - - - - - - - - - - - - - - - - -                             
  
  [ ID] Interval           Transfer     Bitrate         Retr                    
  
  [  5]   0.00-10.00  sec   586 MBytes   491 Mbits/sec  1674             sender 
  
  [  5]   0.00-10.01  sec   585 MBytes   491 Mbits/sec                  
receiver  
                                                                                
  
  iperf Done.

  2: enp3s0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc fq_codel state UP 
group default qlen 1000
      link/ether e4:b9:7a:f7:c4:8b brd ff:ff:ff:ff:ff:ff
      inet 192.168.0.21/24 brd 192.168.0.255 scope global dynamic noprefixroute 
enp3s0
         valid_lft 171856sec preferred_lft 171856sec
      inet6 fe80::781a:829f:5030:ad6a/64 scope link noprefixroute 
         valid_lft forever preferred_lft forever

  $ ethtool -S enp3s0 
  NIC statistics:
       tx_packets: 571053
       rx_packets: 1184934
       tx_errors: 0
       rx_errors: 0
       rx_missed: 1919  <<<<<<<<<<<<<<<<<<<<<<<<<<<
       align_errors: 0
       tx_single_collisions: 0
       tx_multi_collisions: 0
       unicast: 1184926
       broadcast: 6
       multicast: 2
       tx_aborted: 0
       tx_underrun: 0

  2: enp3s0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc fq_codel state UP 
mode DEFAULT group default qlen 1000
      link/ether e4:b9:7a:f7:c4:8b brd ff:ff:ff:ff:ff:ff
      RX: bytes  packets  errors  dropped overrun mcast   
      1785166133 1184970  0       0       0       2       
      TX: bytes  packets  errors  dropped carrier collsns 
      39395440   570500   0       0       0       0  

  on the other side i see dropped packets, maybe flowcontrol-related?

  ethtool reports "Link partner advertised pause frame use: Symmetric"
  but maybe flowcontrol is not working...

  also driver reports flowcontrol is enabled...

  $ dmesg | grep r8169
  [    0.939358] libphy: r8169: probed
  [    0.939491] r8169 0000:03:00.0 eth0: RTL8168h/8111h, e4:b9:7a:f7:c4:8b, 
XID 541, IRQ 128
  [    0.939492] r8169 0000:03:00.0 eth0: jumbo features [frames: 9200 bytes, 
tx checksumming: ko]
  [    0.986853] r8169 0000:03:00.0 enp3s0: renamed from eth0
  [    3.478981] Generic FE-GE Realtek PHY r8169-300:00: attached PHY driver 
[Generic FE-GE Realtek PHY] (mii_bus:phy_addr=r8169-300:00, irq=IGNORE)
  [    3.591124] r8169 0000:03:00.0 enp3s0: Link is Down
  [    7.171198] r8169 0000:03:00.0 enp3s0: Link is Up - 1Gbps/Full - flow 
control rx/tx

  ProblemType: Bug
  DistroRelease: Ubuntu 20.04
  Package: linux-image-5.4.0-29-generic 5.4.0-29.33
  ProcVersionSignature: Ubuntu 5.4.0-29.33-generic 5.4.30
  Uname: Linux 5.4.0-29-generic x86_64
  ApportVersion: 2.20.11-0ubuntu27
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  frank      1427 F.... pulseaudio
  CasperMD5CheckResult: skip
  CurrentDesktop: GNOME-Flashback:GNOME
  Date: Fri May 22 06:49:34 2020
  InstallationDate: Installed on 2020-04-27 (24 days ago)
  InstallationMedia: Ubuntu 20.04 LTS "Focal Fossa" - Release amd64 (20200423)
  MachineType: Dell Inc. G5 5590
  ProcEnviron:
   TERM=xterm-256color
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=de_DE.UTF-8
   SHELL=/bin/bash
  ProcFB: 0 i915drmfb
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-5.4.0-29-generic 
root=UUID=7c9113b7-ca65-4c46-9435-f5d2b73bab72 ro quiet
  RelatedPackageVersions:
   linux-restricted-modules-5.4.0-29-generic N/A
   linux-backports-modules-5.4.0-29-generic  N/A
   linux-firmware                            1.187
  SourcePackage: linux
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 02/07/2020
  dmi.bios.vendor: Dell Inc.
  dmi.bios.version: 1.12.0
  dmi.board.name: 0KW84T
  dmi.board.vendor: Dell Inc.
  dmi.board.version: A00
  dmi.chassis.type: 10
  dmi.chassis.vendor: Dell Inc.
  dmi.modalias: 
dmi:bvnDellInc.:bvr1.12.0:bd02/07/2020:svnDellInc.:pnG55590:pvr:rvnDellInc.:rn0KW84T:rvrA00:cvnDellInc.:ct10:cvr:
  dmi.product.family: GSeries
  dmi.product.name: G5 5590
  dmi.product.sku: 08EA
  dmi.sys.vendor: Dell Inc.

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