Sounds like something is interfering and the most common culprit is an Anti-Virus program.

It may be scanning incoming mail before it allow Thunderbird access and/or scanning any file that gets opened in the profile before anything can get written to a file etc. It can cause all sorts of performance issues.

Compacting means Thunderbird creates a new mbox file eg: Inbox- it then opens the current Inbox mbox file and reads it - anything that does not have a 'marked as deleted' flag meaning anything previous either deleted or moved - gets copied to the new file. Then when completed, the original is deleted and the new Inbox replaces it. This is repeated for all your mbox files = folders as seen in Thunderbird.

When Thunderbird wants to compact all folders - it is advisable to do the following. Put Thunderbird in Offline mode, thus ensuring nothing is incoming, do not select any folder or email or create any emails - just wait and under no circumstance exit/close Thunderbird. The whole process should not take more than a few moments. If you are just doing a manual compact on one folder eg: Inbox, then it's likely to be a couple of seconds. So going offline should not be necessary.

What Anti-Virus are you using ? Advise is to access Anti-Virus and set up an exception to not scan your Thunderbird profile folder or anything it contains.

If you downloaded Thunderbird from the official website: https://www.thunderbird.net/en-US/thunderbird/all/

then the 'Thunderbird' profile folder to exclude from scans is here; C://Users/username/Appdata/Roaming/Thunderbird

When Thunderbird wants to compact all folders - it is advisable to do the following. Put Thunderbird in Offline mode, thus ensuring nothing is incoming, do not select any folder or email or create any emails - just wait and under no circumstance exit/close Thunderbird. The whole process should not take more than a few moments.

But the point is that this happens as soon as I start Thunderbird. At that point I do not want to go offline because I want to download all my messages and I also want Thunderbird to filter the messages to the right directories. But instead I get this message. Do I really want to make Thunderbird an exception for my anti-virus software (it is eSet by the way)? Surely I want it to be scanning incoming emails for viruses.

Emails that contain bad stuff tend to include them as attachments or links or remote content.

Downloading and opening an email in itself does not auto open any attachment nor select and open any link to a bad website.

Only you can click on an attachment to open it and no one should ever open an attachment just because they are curious. Only open attachments if you know they are from a reliable source. Some attachments can look like eg: a pdf but in reality they are not. I get plenty of bogus attempts to say eg: invoice ia attached when I know I've not ordered anything. Best advised action is delete the email and then compact folder to fully remove from files.

Thunderbird by default does not allow any Remote Content, that option can only change if you deliberately activate and allow it to occur.

• Settings > Privacy & Security
• Mail content
• Advise is - Do not select this: 'Allow remote content in messages'

More info on Remote Content:

• https://support.mozilla.org/en-US/kb/remote-content-in-messages

AS for links which may be appear as text or look like a webpage link or be included in an image etc. Never click on a link which may appear as ok until you have checked if it is correct and expected. How to check a link ? Hover cursor over link (do Not click on it) and the real link is displayed in the bottom Status bar.

You are more likely to get a virus auto downloaded by accessing a bad webpage which hopefully your AV is checking as well.

I've had plenty of emails pretending to be from a legit company and the link in email that looks ok, when you hover over it, the real link is obviously very wrong.

Even if you want your emails scanning on download, you do not want your profile folders and files being scanned when Thunderbird wants to write to them or scanned during a normal scan.

Even if it finds something is wrong in a thunderbird profile, you never want it to perform an auto fix because no Anti-virus understands that an mbox file is likely to contain a lot of good wanted emails, it thinks there is only the one and a fix on the mbox file will probably delete everything in it. An mbox file in profile = a folder in Thunderbird UI.

Frequently, if AV finds something, the odds are you have already deleted that bad email, but not cleaned up the file, so AV is detecting a 'marked as deleted' email. Compacting the folder will remove it and sort out the problem in a manner that does not effect other emails in same file.