Ok, here is some more information and possibly a solution:

One of the apps I run is ASG Remote Desktop. This app allows for RDP, RDC, VNC, SSH, and external apps such as Java and browser based apps to be run in a tabbed Window.

I have two db's and two environment files, one is ASG - Remote, and the other is ASG - StorLab. When I click on the shortcut to start the ASG - Remote main environment, all works as it should. I had the application setup to run in Desktop 3.

When I click on the shortcut to start ASG - StorLab, it automatically started vCenter Web Client, which is a Web/Java app. I had a rule to move this app to Desktop 6 based on the Window title. The app brings up script and security pop-ups, which always went to Desktop 3, to the auto-assigned desktop for the app. I would switch to Desktop three and clear the notifications, then switch to Desktop 6, but ASG-RD would not accept any input via keyboard or mouse. The only thing I could do is bring up Task Manager and kill it.

To make a long story short, ASG-RD has an option in the database section to start the App in a separate instance. I also took out the Application assignment, and added two rules based on the Window title. Now when I start each application, the main app goes to Desktop 3, and the StorLab app goes to Desktop 6. However, the pop-up still end up in Desktop 3, but I can switch and clear them and then switch back to Desktop 6 and continue running vCenter Web Client without ASG-RD locking up.

However, I need to figure out how to do the same thing with my web apps which run in IE. I have shortcuts to those URL's in my taskbar, and sometimes when I start one of them up, it pop-up message, and when I clear it, the IE app window is locked. I guess one thing at a time. Hope this helps anyone else who may be having a similar issue.

I've experienced an issue where child windows from an application will pop-up briefly, then change to another desktop. However, they do not appear in the new desktop. The Taskbar shows the child window, but nothing I do will make it appear.

Looking at the forums, I've looked at the hidden windows, but the window in question is not in the hidden list. In fact it shows up on the desktop list. I just can't bring it up or do anything with it except close it.

Examples:

Outlook 2010 on Win7 x64; in calendar, create new entry.
Calendar entry opens, and I start creating meeting and adding invitees
I then click on Scheduling Assistant; I see the window pop-up, then it moves to another desktop
Clicking the window in the taskbar will not bring it up
Following to the desktop it switched to, (usually 2 in this case) does not help
The Scheduling assistant window shows under the Outlook group in the taskbar, but I can not make it appear

I open an IE URL via a shortcut to a site using IE 11
IE pops-up with an error about compatibility, or login authentication
The pop-up switches desktops
In this case I can follow it and resolve it, but when I go back to the original IE window it is blank and any control I try to access simply beeps; I cannot even close it from the taskbar. In most cases I have to close all iexplore processes.

Has any one else encountered this, and is there a solution?