Hi @Tom Wardrop ,
According to the document below, "In Exchange Online, the message is moved to the Junk Email folder if the junk email rule is enabled on the mailbox (it's enabled by default).".
Configure anti-spam policies in EOP
So I'd recommend run the command below on one user mailbox and see if junk email rule is enabled:
Get-MailboxJunkEmailConfiguration -Identity "<MailboxIdentity>" | Format-List Enabled
If it's indeed in the enabled state, try disabling it and check the result:
Set-MailboxJunkEmailConfiguration -Identity "Ori Epstein" -Enabled $false
If it works, you can disabling the junk email rule for all users using:
$All = Get-Mailbox -RecipientTypeDetails UserMailbox -ResultSize Unlimited; $All | foreach {Set-MailboxJunkEmailConfiguration $_.Name -Enabled $false}
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