Do you have an suggestions on what I should look at to try to get it working?
EDIT: I found the problem.
I was using Subject->Begins With - the regexp created by ISPConfig for "Begins With" is:
### BEGIN FILTER_ID:1
### END FILTER_ID:1
That will never be true, since there is always a space after header fields, in this case "Subject:". When a space is added between "Subject:" and the pattern, "Begins With" works fine. My opinion is, this is a bug, unless I am missing something. Note that if you specify "Contains", it works fine because the regexp is correctly formatted. I did not try the other tests.