Skype (probably on its update) re-register "HKEY_CLASSES_ROOT\callto\shell\open\command" to "C:\Program Files (x86)\Skype\Phone\Skype.exe" "/uri:"%l"" (previously callto: links starting click Phoner).
 
Trying to register back to Phoner, by checking on option "URL handler" on "Options -> Web" does not change anything. Tying few times check/uncheck, restart phoner, but it registry item remain unchanged. What am I doing wrong? Version 3.01