Filters does not like Unicode with BOM format files. I was using Set-Content -Encoding utf8 for generating the filters file, and upon debug the first filter is corrupt (extra spurious chars at beginning)
Filtering a junction (mklink /J) is not treated as a directory
myjunction/ does not match
So to include a set of descendent folders I had to
These had me stumped for a while. The duplicacy -log -d backup -dry-run command was very useful in finding out what was wrong.