I am on EU servers, but I've found that using Restore N' Patch.exe only causes problems.I have the same issue, (I'm using JP server btw
Whenever I've downloaded updates, I just use resorepless and meta injector to patch the files again.
My Paz folder contains folder > Source_Codes, pad00000.meta and the meta.backup. all other files used when patching are deleted.
Try the patch process from scratch and don't use restore N' patch, maybe that could work.