1. I have sections of code collapsed with outlining on
2. I hover over some collapsed code so the yellow tooltip shows
3. I click on the Windows task bar and foreground another application
4. The tooltip is visible above the new application
5. I have to return to EmEditor and move the cursor to some visible code to hide the tooltip

How are you getting the tooltip to stay on screen after clicking on the taskbar? The only way I can get a tooltip for collapsed code in EmEditor is to hover over sections in the outline plugin... and the only way to keep the tooltip from disappearing when I move the mouse away is to right-click. Even if I am able to get another application open/active without the tooltip disappearing -- the tooltip is underneath the newly activated window, not on top.

Compare that to Opera 10/11, where if a window like Total Commander is on top of an Opera Window - the Opera tooltips (e.g. Yahoo Mail) get activated all the time and show inside the TC window. This is all due to Opera using proprietary GUI controls that don't respect MS-Windows rules.

well sometimes it happens because a script running on one of my web pages launches a new window, r I alt-tab to Excel

I found it's quite easy to reproduce this issue:

1. Hover mouse cursor over the collapsed block of some code, the tip will appear.
2. Press <Alt> + <Tab>, switch to another window, the tip will remain on top of the screen, make some area inaccessible.
3. Switch back to the EmEditor window, and move mouse cursor, the tip dissappears.

Please watch my screencast.