On the Settings > Search tab, enable "Treat all exclude path filters as wildcard," then just put the sub-folder name in the "Exclude Path(s)" box when searching. It seems that Exclude Path(s) is broken when the "Treat all exclude path filters as wildcard" option is disabled. I've added this to our list to fix up
Last month we released FileSeek 5.1 (http://www.fileseek.ca/Download) and this issue should be all fixed up. Please let us know if you run into any trouble after updating.
