Anderton
This also appears to be intermittent. I tried to duplicate and couldn't, but then I could.

this is possibly the most troubling aspect of any bug, in that it implies the bug is "low level," or "far away" from the observed symptom...  i wonder if it's related to the "history/undo" issues?

This is definitely a problem.  It seems that Sonar is forgetting how to use the right-click, drag and highlight feature, which I use all the time.  Here's how to replicate it:
 
1.  First create a track with A) some audio FX in the Bin, and B) an audio clip in the actual track.
2.  Now, click inside the FX Bin, or click an actual FX plugin to open it, as if to mess around with it, then close it.
3.  Now right-click and drag "sweep" to select the audio clip(s) to highlight it with the glowing-blue box.
4.  Let go of the right mouse button.  The audio clip should be highlighted/active.
5.  Now press the delete key.  The FX plugin that had the brackets around it will be deleted.
 
UPDATE:
 
I just tried it in X3e, and the behavior is the same.
I just tried it in X2a, and the behavior is the same.
I just tried it in X1d, and the behavior does not exist because the right-click "glowing-box sweep" select does not exist.
 
So it appears we've been living with this buggy behavior since the X2 days.

I think that's what I said earlier.
 
It seems like when using the right mouse button to perform some action, eg lasso a number of clips, it does not override the previous "in focus" state for the plugin which would have been the last element to have been activated with a left mouse button action. I've tried it and that seems to be the case.
 
If I make a deliberate left mouse click on any one of the clips before I lasso them, then when using delete, it deleted the appropriately lassoed clips.
 
Something about right mouse button activity that I remember reading in a previous thread that seems to be of the same or similar nature.

seems to be to do with "selected" versus "focussed" and the right mouse button doesn't instantiate what's expected

mudgel
I think that's what I said earlier.

I must have missed it.  Sorry 'bout it.  Did you report the issue?  I think this needs to be squared away by Cakewalk.