The difficulty of troubleshooting this along with the fact that no other users have had similar complaints in over a month should indicate that there is something unique to your situation.
To recap, here are the relevant facts:
at primary location:
sys-whonix -> ??? -> sys-net:
conclusion: unreliable Tor connectivity at primary location using sys-whonix
at other locations:
sys-whonix -> ??? -> sys-net
at primary location?:
debian-9 -> ??? -> sys-net
tor bootstraps properly.
loses connection often? or not?
win10 -> sys-firewall -> sys-net
conclusion: unknown. now is a good time for extensive tests
There are too many questions there still. You need to test thoroughly and provide detailed information. At this point, I’m not convinced this is a Whonix issue.
If you have unreliable Tor connectivity at primary location and it works elsewhere, then it’s clearly a problem with your ISP, LAN, or network hardware. You need to get support from your hardware provider or ISP.
If you have unreliable Tor connectivity at primary location using Whonix but Tor connectivity is reliable using Debian template or Windows 10 through same network connection, then that would be very strange indeed.
Where do you want to install a packet monitor? Do you think packets are being lost between Qubes VMs? You could simply see packet counts using
iptables but I highly doubt that Qubes networking is the issue here.
(Also, I have no idea what ubiquiti is. Are you using wireless connections?)
Here’s a better test. Since you’re using Qubes, do this at the same time.
anon-whonix -> sys-whonix -> sys-net
get tor bootstrapped in gateway.
launch tor browser in workstation and download some big debian .iso.
win10 or debian -> sys-net
install tor browser bundle
launch tor browser and download some big debian .iso.
If 2 works and 1 doesn’t, then we have a problem.
If neither works, then test using a different network connection and/or a different network.
If both work, then hooray.