I forgot to add code to bypass this progress dialog (feature introduced in a recently release), when running in silent mode. I will have this fixed in the next release.
This progress dialog is shown when the tool is checking the PDFs to be merged, gathering the total number of pages and checking file validity. At this time it is not merging the files yet. I've added this because, when running in GUI mode and the number of selected files is considerable, there was a non-visible activity delay before the tool showed up the GUI, tricking the user to think the tool failed to start.
Thanks for reporting.