Which means you're running the command from a different location. It needs to be run from the exact same location where the server file is located.
OK now when I run the server this happens http://pastebin.com/yKQBwwxK and it deletes all of my modded blocks. I luckily made a backup before this but I really don't want to have to place all of my modded blocks again because it would take at least a week of replacing blocks.
Though this happened when I hit the main server button the BAT file with more ram still does not work