Your computer seems can't store Similarity configuration file and each time it uses default settings.
1) Please send us log files from "%appdata%\Similarity\logs" folder (enter in Explorer).
2) Please try use Similarity in portable mode: copy folder from "c:\Program Files\Similarity" to "My Documents" or other writable folder and create shortcut to Similarity.exe in this new folder, add "-portable" command line after.
