Sent mail is stored in Sent Mail for gmail, but outlook.com stores it in Sent. Both providers automatically copy sent messages, so uncheck 'Place a copy in' in Account Settings, Copies & Folders. You should see a single copy in Sent, but the changes you made might have upset things. Perhaps try unsubscribing Sent, restarting TB, then subscribing Sent again.

Corrected Update - and this does seem to be a Thunderbird problem, not an Outlook one. [n.b. in my earlier Update, I suggested that the difference was between Replying and Sending a New email; apologies to those who replied based on that post of mine.]

On our PC, under Account Settings the Default Identity is of the format AandB.Surname@outlook.com; under Manage Identities, we have set up individual identities of the format ASurname@outlook.com and BC.Surname@outlook.com Replies to all these addresses arrive at our PC - now, as previously, so Outlook is working properly. When sending (or replying to) an email using the Default Identity, only one copy is sent; when using one of the individual identities, Thunderbird puts two copies in the Thunderbird Sent folder - and Outlook receives these two copies. (I don't normally look in the Outlook "Sent" folder, just in "Junk" but today I did and noticed what has happened.) This change of behaviour by Thunderbird has occurred since recent Thunderbird updates.

Apologies sfhowes - I hadn't seen your reply when I wrote my update. Unfortunately, it doesn't seem to have solved the problem; I did as suggested [un-checked "Place a Copy" in Account Settings, Copies & Folders, un-checked Sent in "Subscribe"; closed & reopened TB and re-checked Sent. I sent a test message and have two copies in Sent.

I configure my Gmail accounts to save a copy of sent messages (in addition to the copy that Gmail saves automatically), but I tell Thunderbird to use a Local Folders 'Sent' for that, so the copy saved by Thunderbird and the one saved by Gmail are kept in separate folders. You may want to do the same with this account, at least temporarily, just to see who is doing what.

Just to confirm - I'm using Outlook - not Gmail.

I know, I didn't mean otherwise, but both Outlook and Gmail appear to work similarly in this regard, i.e. both save copies of sent messages on their own, so I used what I do with my Gmail accounts as an example of what you may want to try with your Outlook account, just to see who (i.e. whether Thunderbird or Outlook) is doing what, and you don't try to fix in Thunderbird what Outlook is doing and you have no control over.