I use the standard BT anti-virus softare, Network Protect from McAfee
I have not yet disabled it as some (but not all) emails are getting through, which makes life complicated!
It may just be coincidence, but I note that the messages that don't get through do not follow my filter rules when they are forced to download by restarting Thunderbird. Those that do get through seem to follow my filter rules
You could try a different mail client. Stop T'bird and temporarily and try installing EmClient or Claws Mail and see if it is any different.
Thanks for your suggestions. I have reinstalled Thunderbird twice, with no improvement. I only have one Rule set up, and that does not always work. For security reasons I am reluctant to turn Firewall off. As it is relatively easy to get round the problem by exiting and re-entering T'bird, I am inclined to live with problem for the time being, rather than download another email client