Selecting notes was working fine in Sonar X2 and then something must have changed because now when I drag select  (either with the smart tool or select tool) it selects the whole time range instead of only selecting the notes I drag the bounding box over.  This means there's no easy way to select notes without also selecting the notes above and below them.
 
Is there some setting I accidentally toggled that would cause this?

Actually, it looks like it isn't just drag selecting.  If I individually select two notes  by holding shift LMB it will also select all the notes in the time range between those two notes.

Also, when I restart Sonar X2 the selecting works normally for a minute and then after dragging notes a few times it starts doing the weird dragging behavior again.
 

this works fine, make sure your selecting only the notes you want.
right click and drag lasso the notes you want to edit,
then make sure your snap value is set properly or it will drag by increments of, 18/ 1/4 1/2, exc.
what ever your snap is set to.
 
how are you editing/selecting notes ?

If the controller pane is closed and you're touching velocity tails or other notes in the notes pane, those notes will be included in the selection by default. See page 739 of the X3 Ref Guide for the registry edit to disable this. Or just show the Controller pane so velocities aren't in the notes pane.

Oh man!  Velocity tails was the issue!  That's why the problem seemed to come and go, I didn't realize sometimes I was or wasn't dragging over the velocities.  Thank you for the help!  And for the registry trick, I'll probably make that change down the line.