I'm a heavy lasso-select user and have encountered the very issue a few times in the past. So, it's not a new behavior.
Unfortunately, you can only guess that the focus is still on the FX bin when the clip didn't get deleted and hit undo to bring back the plugin. I know, it shouldn't happen in the first place, but I don't think the behavior will change in the next.....few years, at least.
 
I frequently use the right-hand lasso even when I only need to select a single clip. This is because, with the left click, my hand could easily slip a bit and move the position of the clip a very little without noticing it. You might think that I should use the Lock Clip Position feature, but it not only locks the clip position but also disables the Nudge feature (which I want to use to  nudge note events up/down in the clip) and also CAL commands (which I want to use to change velocity values, etc.)
It's an officially confirmed bug.
 
 

Hey Tak T,
 
Ok, now it's all becoming clear. Since I started using right-hand lasso (about 2 years now), I no longer move clips by accident. (So like you Tak T, I also use it exclusively to select a clip). And that's when I started accidentally deleting plugins (but without knowing how or why). Thanks to this forum and to everyone who has provided feedback, I've already caught it a few times and I'm able to undo (control+z) my way back. I really do hope there's a fix someday. As sometimes (by the time i figure out the plug is gone), it's too late to undo.
 
So here's a helpful hint for anyone who might run into this problem:
If you lasso a clip (or clips) and you press the "delete" key, and the clip does not delete- THEN you've just deleted a plugin. So press "Control+Z" and then left click anywhere in the trackview (this deselects the plugin). Now you can lasso any clips and delete away.
 
Thanks again to everyone, this has been a tremendous help to me.
 
Serg
 

 
So a clip is selected, then you open and close a plugin, and then expect the selected clip to delete if you hit delete.  I don't feel that this is a natural assumption since any number of things may have happened since selecting the clip.  Reproducing this problem, I wasn't surpised the clip doesn't delete, and I can understand the plugin disappearing since it's the last thing that was clicked on (though I agree it may disappear without your noticing).
 
Deselecting the clip when you click on something else would make sense to me.  It's odd that this doesn't already happen.
 

djserg
...If you lasso a clip (or clips) and you press the "delete" key, and the clip does not delete- THEN you've just deleted a plugin.

I'm not sure how you could literally select a clip, press the Delete key, and not have the clip deleted. 
Unless as Paul stated there are other steps used in between...?

@Paul & Steve:
 
You can easily reproduce this, regardless of track type (audio/MIDI):
 
1. In the Track view, click an effect in the FX Rack. This will open the plugin window.
2. Lasso-select any clip in the Clips pane.
3. Hit Delete.
 
The effect in the FX Rack and the effect's property page disappear (get deleted) from the project.

I think using the right mouse button to open a context menu doesn't place the underlying clip in focus thus leaving the previously edited plugin still in focus, hence the delete plugin not clip delete.

It is not for a context menu but rather a lasso to select the clip (intent to shift focus, but doesn't take). Try what TakT posted and you will see.

icontakt
1. In the Track view, click an effect in the FX Rack. This will open the plugin window.
2. Lasso-select any clip in the Clips pane.
3. Hit Delete.
 
The effect in the FX Rack and the effect's property page disappear (get deleted) from the project.

It does indeed.  This is definitely wrong.  Selecting the clip and hitting delete should delete the clip.
 
This must explain why it has often happened to me that I selected a clip but then couldn't for the life of me delete it with the delete key.  I then wondered why sometimes it worked and sometimes it didn't.
 
It has also happenend to me (in fact while trying to reproduce the first post to this thread) that my plugin is selected in the fx bin but it won't delete with the delete key.
 

Yep! Same problem: http://forum.cakewalk.com...-My-Pain-m3333681.aspx
 

2. Clip deleting by Del key doesn't delete the clip, but delets a plugin in a FX Bin. Why for G's sake should it do that?
This problem is easy to reproduce. After any operations in the FX Bin, select any clip(s) by rignt mouse button lasso (Smart Tool) and press Del on your keyboard. Voila.
Guess how many times I unsuccessfully tried to delete the clip, and then from my memory I tried to restore the order and settings of plug-ins? I do it all the time...

 
 
Guys, please, if you have the opportunity to leave CWBR request - do it! The only way we can solve our problems, but not a separate messages on the forum.
With faith in the best.

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