I tend to scan and save in batches, which is why I find the current settings useful. However, I see that other people might have different workflows. I could add an option to blank the metadata when a new scan is made.
gscan2pdf should already import a scanned PDF from a fax service. Please try.
gscan2pdf currently uses PDF::Builder, not PDF::CREATE. It used to use PDF::API2, but I switched to PDF:Builder to improve the TIFF compression options. I am currently in the middle of a complete rewrite in Python. This should offer lots of advantages, including PDF/A support.
If the image is .jpg, then automatic compression will also use jpg for the PDF, and will take the quality parameter from the last time a jpg or a PDF with jpg compression was saved. i.e. if you save a test PDF compression=jpeg with quality=90, then that value will be used by subsequent PDFs with automatic compression that are jpg internally. Note that the DjVu compression method also depends on the image type - jpg/png uses c44 (although I really should get around to also implementing cpaldjvu)....
You are using quality=66 when creating the PDF. I suspect that higher values will produce PDFs that are larger than the DjVu. The image in the DjVu is compressed using c44. The quality settings in c44 are not a simple as percentage. I could expose them, but I doubt most users would take the time to try and understand them. Have you seen the c44 options?
Thanks for the log file. It looks as though you have set "frontend" to "scanimage". Try using "libsane-perl". Brother seems to have given you two drivers, one via the network, and one local. I would try both of them.
Please start gscan2pdf from the command line with the --log=log: gscan2pdf --log=log then open the scan dialog, quit, and post the log file, which gscan2pdf should have compressed with xz
This is a sign there is something very weird happening, as normally $line can't be undefined if the watch has been triggered. Please apply this patch and see if we can work around it