Hello I have Sonar X3e
When I edit a track in Melodyne and then edit a second track in Melodyne both tracks are affected by what I do. Even thought hey are both separate Regional Effects

I have Melodyne Editor 4
I used to be able to do this without any issues - Hopefully it can be fixed otherwise I will regret not getting the melodyne studio upgrade for $150.00

Thank you

you could? I always thought that multi track editing was only possible in studio. You could edit 1 track, render it, then edit another.
(I would make acopy of the unedited track before doing any of this , just in case.)
 

Open one track in Melodyne and select clip view. Then open your second track in melodyne with the ctrl key pressed. This should give you 2 tabs on the multidock of your melodyne tracks. The Editor is only open once but you can switch between tabs to edit different tracks.
 
Full multitrack editing is only available with the studio version.