Hey there. This is happening again. I have few software synths open, I want to delete synth. I press delete synth button, it usually opens "Delete associated tracks?" Well- this dialog box is hidden under windows, so dont matter where I click in Sonar, I hear Ding Ding, but I can not get to dialog box, and I can not even close Sonar. So far I only can restart computer to get out of it. How do I fix it? Thank you. 

Dock your synths rather than float them.

Also check the Task Bar. There will usually be something there alerting you to a dialog box. Click on it to make it visible.

Press and hold the alt key, then pressing the tab key should cycle thru any open windows, dialogs.  This may help.

Thank you for your replies. I have my synths on another screen, but it happens disregarding of where the synths are. I found what causes it. I have Kontakt open with Sequence Hip Hop Beat Creator. It must be poorly written because it causes transport not respond correctly (Stop button is grayed out- see my other thread if interested), and now this. There is no dialog box opening. I thought it is under the synths, but it is nowhere. Not on any of my 5 monitor screens, not under software synths. The Kontakt eats it when it opened (but only when Sequence is loaded). I would like to know the mechanism of action for this problem- Big Fish Audio needs to know this. I had to restart computer like 5 times trying to figure it out and last time it cached Windows update, so it was sitting at "Getting your computer ready" for like 10 minutes- it is uncomfortable when it happens after you forcefully restart computer with open application like Sonar. Also when restarting, it does not even say, "Would you like to Save"- like Sonar not even open- just restarts. So it is Sequence problem. Thank you. 

I'm having the same general problem and would appreciate anyone who knows how to fix it. 
 
In Platinum, anytime I close an instrument in Kontakt 5 (which is pretty often), I get a "Save Changes to Instrument" dialog box.  The box started opening underneath Kontakt a few weeks ago and generally drives me nuts.  I have to use the alt tab key to get at it.  I don't have room to move the Kontakt screen over all the time (single monitor).  I can't get it to go on the Multidock for some reason either, although I don't think I would use that placement anyway-- it's height is too limited.  The best would be to shut off the dialog in Kontakt, but I can't see where to do that.  
 
Anyone?

Yea Kontakt has had this issue for years.

If you know what the hidden dialog is asking you, and know what the default choice is, just press the Enter key.
 
If you don't know what the dialog is doing, press Alt-Tab to reveal it. 
 
Unfortunately, this phenomenon is going to crop up now and again in any windowed GUI. Windows normally does a good job of keeping track of Z-order and focus, but programs routinely mess with the scheme for their own reasons. For example, a program can instruct Windows to always keep its window "on top" of everything. Enforcing Z-order is what keeps Kontakt from disappearing behind the DAW's main window, and lets you float the Transport over the track view. But multiple such instructions can conflict with one another. Windows tries to figure out which high-priority window actually needs to be visible, but it isn't always 100% successful.
 

I've had this problem for years with Sonar and NI plugins.  The NI main synth UI window will be open, but it will pop up a dialog box behind the synth window ( usually asking for a path to samples or somesuch ) and there is no way to click it without rapid alt-tabbing and keep hitting the ENTER key hoping it will land on the correct window.
 
Same computer, same plugin, doesn't happen on Reaper.  I assumed it was some setting within Sonar that controlls the "stack" of windows opening up but I have not been able to find it.
 

Thanks for all your replies.  It only started a few weeks ago after working properly for about 8 years.  So I'm guessing it's either a Kontakt update or a Windows update.  I didn't do the Sonar updates for many months.  
 
Bitflipper - thanks for your post.  Pressing Enter does a Save, which I hardly ever want (that Save overwrites the preset).  However your suggestion made me think.  If I hit the right arrow key, then Enter, it always answers No, (don't save).  So that works perfectly and is only one extra keystroke.  So that works pretty well, thanks!