Is that second copy in Archives or All Mail? The latter is a gmail construct that contains all messages, received, sent, deleted etc., and is usually not subscribed in TB. Archives should only contain messages that are deliberately placed there, unless you have a filter to do so.

TB shows them in Archives and when I mark the mail as read in Inbox, there are a couple of seconds of delay before the one in Archives also becomes "read".

I haven't done anything to the GMail account settings or filters since adding my GMail. I have added a second GMail account a couple of days ago and it has the same behavior.

I also noticed that emails get the Unread count in the Archives first as the emails actually appear in the Archives before they do in the Inbox

New messages appearing in Archives is not normal, even for a gmail account. I suggest you create a new profile, add a gmail account, and see if the pattern remains. Help/Troubleshooting, about:profiles, to create and manage profiles.

I did re-create everything in a new profile and so far it seems to be working perfectly! Thank you very much. After I started adding the addons I used previously, I skipped one: https://addons.thunderbird.net/en-US/thunderbird/addon/gmail-conversation-view/?src=search

Wonder if it could be the reason for this behavior?

Launch your original profile from about:profiles, disable Conversations, then restart in that profile and see if it caused the issue.

It didn't fix the problem and, unfortunately, even the new profile reverted to the same behavior. Now emails are shown three times. Once in the individual inbox, another time in the combined inbox and a third time in Archives. See attachments.

It is normal for new mail to appear in the Unified Inbox as well as the individual Inboxes, but not in Archives. What other apps are running at startup, such as antivirus, online backup etc.? Right-click the Start button, Task Manager, More details, Startup tab. What are the add-ons in the new profile?

See attached the addons enabled with this new profile. I do not have any antivirus (just Windows Defender). I use OneDrive and NextCloud and also have KeePass, Mozilla VPN, Firefox, Rocket.Chat and WhatsApp for Windows running. Nothing else.

I don't see any add-on that would cause messages to appear in Archives. As long as you aren't storing the profile in OneDrive or NextCloud, the only other apps to examine are KeePass, if it's managing TB passwords, and MozillaVPN, as VPNs can create issues with TB. You could test the effect of startup apps by running Windows in safe mode, to bypass those apps.

Nothing changes. Tried with no running apps and Thunderbird continues with same behavior.