I have checked the "delete empty folders" option in the main screen and still the program doesn't delete the empty folders. Otherwise this program rocks. Let me know if there is a solution to this.
This option is v2 only affects folders, which becomes empty after SynchronizeIt! deletes files from it. Folder which were empty before are not handles by v2. I recommend you upgrade to latest v3 - it can handle (optionally) empty folders as other files.