Ok, I have just done a complete re-test and confirm that it seems to be
working for me now.  To be clear, my (previously failing) test was:

1, Receive an email that may have custom headers in it. (eg, X-customheader-set)
2, set up a message filter to look for and action on that customer header 
(X-customheader-set)
3, Run Manually the new filter

The result was that the filter didnt detect the headers.

HOWEVER....  after reading this  I see that Thunderbird needs to have
the CUSTOM HEADER already defined in the Message Filter Setup (and
therefore begins to record the occurrence) of the header prior to the
messages being received.  It is because the customer header is being set
up AFTER the message arrives that it is not being found.

SO THE SOLUTION IS:

After you set up a new CUSTOMER HEADER (in Message Filter setup) to
search for in the Filters List, you need to do a 'Folder Repair' (which
rebuilds the MSF file for the folder) on the folders concerned.  This
then forces Thunderbird to record the existence of the custom header in
the MSF file and you will then see that the messages are actioned
accordingly to the new filter.  Also, any NEW messages received AFTER
THE CREATION of your customer header will be actioned on automatically
(according to your filter definition)

So, to set up a NEW filter for Custom Headers on existing messages, the
process should be:

1, Receive an email that may have custom headers in it. (eg, X-customheader-set)
2, set up a message filter to look for and action on that customer header 
(X-customheader-set)
3, do FOLDER REBUILD on the folders that you will be running this filter 
against.
4, (Manually Run the new filter if you need to - depending on your Filter 
definition)
5, Any NEW messages with X-customheader-set will be actioned accordingly as per 
your Filter

For me there is now no problem regarding this 'issue'.

Using TB 31.6

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https://bugs.launchpad.net/bugs/119899

Title:
  After-the-fact Filters on custom header won't match for IMAP messages

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