Message filters move mail from all folders

I have a message filter in place that moves all mail from the inbox to a certain folder from where it then gets sorted. After each of the recent thunderbird updates it has moved all mail from all folders including sent & deleted etc into the folder, which causes a real headache. I haven't run the filter on these folders. I have changed the filter so that it only filters mail which has an age in days of less than 1 so I have less work to do to sort all of the mail out. Hopefully someone has experienced this before and can advise on how to resolve this issue. Thanks Martyn