One of the common problems that most people seem to be getting is that when the patcher completes, the resulting file is much smaller than the original ISO. I believe I have found a solution to that particular problem.
Try moving all the patch files to a lower directory and renaming your ISO something short. This might be a problem where the directories get too long for the patcher to handle. If I attempt to use the same patcher from the download, but attempt to patch with the files on the drive in a long directory, it produces the ~670MB ISO. However, it patches just fine if I create a new folder on my desktop and ends up creating a 1.64GB ISO. Remember to have the windows .NET framework and Java installed on your computer as well as at least 4 GB of open harddrive space.
The two “File Not Found” messages that display in the command prompt window are normal, ignore them. Normal procedure on my machine is that the patcher opens JPCSP, appears to do nothing for about 5 minutes, then closes JPCSP and moves on to step 2, whereupon each additional step goes by smoothly, if slowly. The final patched ISO will be named exactly the same as your original one, and the original one will have a .bak appended to the file name.
This patcher will not work with prepatched versions of the game that contain an eboot.old file or prometheus.prx file.