For your Information
PDFToolkit doesn't work with El Capitan, Apple has done some changes that affects PDFToolkit. If you have PDFTK in your flow the files will stop in the folder before the Execute Command element and sort of hangs. To close the flow you have to kill the PDFTK in Activity Monitor.
There is an update/Fix for this from PDF Labs that solves the problem.
https://www.pdflabs.com/tools/pdftk-the ... -setup.pkg
Jan