I'll got an error when using the 'Clean up' function.
After adding two files, I've started the 'Clean up' and just set the layout to 'Double', the '# Output pages' to 2 and started the process.
I've attached two logfiles. One from gscan2pdf (gscan2pdf.log) with the --log function and a second one (mygscan2pdf.log) with the same option but also wrote the stderr into the file so you can see the error output from unpaper.
If I can help you with any other informations, plz let me know.
Thx a lot! :-)