Some emails are auto archiving without going into my inbox but not all. Even the verification email for the community registration did. The auto-archive box in settings is unchecked for the email address. This is only happening on one address and I can't see any difference between the settings.
How are you accessing your email, is it using an email client/app and if so which one?
What devices are you using to access your email?
It doesn't seem to matter. It happens on Outlook 2013 on my laptop and my phone via the Google Mail app.
As BTMail, using webmail does not have the Auto Archiving feature and you are using these email clients/app I would suggest that you go through every setting on them as it would appear that it is one of them that is causing your problem.
You may be able to narrow it down by turning off one of your devices in turn until you establish which device is causing it.
I found an answer myself. In BT Mail I had a folder in the My Folder subset into which some incoming mail was going, but not all. I removed the folder and all mail now goes into the inbox. Why some mail went into that folder automatically would be good to know.
Because you had set up a rule in one of the clients for it to do so.