Great, but if the files are not the problem the only issue I'm aware about the tools when running from PDFE build 58 is related to Unicode directories/filenames, so, if in your case you have one of these situations, Unicode directory/files names, just create a Ansi only directory, e.g. C:\Temp, copy there two of these files and give them a name with only Ansi characters, e.g. File1.pdf and File2.pdf. Check if now the tools work with these files.