When “Configured Encoding” is selected in “Find in Files” dialog box, EmEditor uses the encoding configured in the File tab of the configuration properties assiciated with the file extension you are searching. In default, Text configuration uses “System Default” encoding with UTF-8 and Unicode signature detection. The UTF-8 detection can make search slower. If the “Detect All” is also checked in the File tab of the configuration properties, it may become even more slower. Please let me know which options are checked in the File tab of associated Configuration Properties.
Also, in what encoding do those files you search are encoded? UTF-8 or Western European (CP:1252) or any other?