I often clone tracks if want to record a new track with the same input and settings. But latley, after the last update (I believe), the new cloned track is completly tied to it's parent track. Mute, record, volume and a lot of other controls acts like they are in a goup, but they are not. I wonder if there is a setting I have missed. Never seen this before....

If you are cloning simple instrument tracks, this is nothing new. There are some lengthy threads about it such as http://forum.cakewalk.com/tm.aspx?m=2856182&p=3. Split the track before cloning.

You are probably already aware of this, but there is a checkbox in the clone track dialogue that says link to original. Make sure that this is unchecked. I believe Sonar remembers the state of that particular selection from your previous use.