This was bad news as the system received hundreds of emails per day with a good percentage of it being spam. There had to be an explanation for this; And there was. Kaspersky Internet Security 2009 was previously installed on the test system. The security program made use of an anti-spam module which checked all incoming emails for spam. It integrated itself nicely into Mozilla Thunderbird at that time.

After uninstalling Kaspersky Internet Security 2009 the junk mail controls stopped working in Thunderbird. It was an almost sure bet that this was related to Kaspersky. To verify this assumption the software was installed again. It turned out that the mail filter in Thunderbird started working again after the installation completed (even before a restart) which confirmed that the problem was related to Kaspersky.

The next assumption was that the email client Thunderbird had to be closed before the uninstallation of the security software. It could have been a rights-problem that the uninstaller could not edit Thunderbird related files that were in use on the system.

After closing Mozilla Thunderbird the uninstallation of Kaspersky Internet Security 2009 went through without problems. The important part however was that the Junk Filter in Thunderbird was still working as intended.

To see a broader picture: It does not necessarily have to be Kaspersy Internet Security 2009 that causes those problems after uninstallation. Basically any application that interferes with the junk mail filters can cause a similar problem. Good to know that it can be solved that easily.

Update:

There is another option if that is not working in first place. All you need to do is disable the anti-spam module in the Kaspersky software to disable it before uninstalling the software. This way the Thunderbird junk filter will keep on working after the uninstallation.

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