Does the avast email scanner work with thunderbird as it only says outlook when I have looked at it via on access protection control and if it does what do I need to change (setting wise) as it is saying waiting for a sub system to start at the mo when I run thunderbird

Yes it does, don’t let the Internet Mail name fool you it is for pop3 email clients like Thunderbird and many others and has nothing to do with webmail.

The Problem you are experiencing is because you have enabled the Outlook/Exchange provider (off by default), which is for MS Outlook (not express). So terminate the Outlook/Exchange provider and answer Yes to the pop-up question and the ‘waiting for sub system’ message should be gone.

If you use Outlook (not the Express), when you open it, avast Outlook plugin will be enabled and the message will be gone too.