Does this happen also when you use a newly created uedit32.ini instead of the upgraded uedit32.ini?
To verify this copy %appdata%\IDMComp\UltraEdit into the address bar of Windows Explorer and press key RETURN or ENTER to open this directory containing the configuration files with your UltraEdit settings.
While no instance of UltraEdit is running rename now uedit32.ini to uedit32_bak.ini (contains most configuration settings) and also uedit32.in0 to uedit32_bak.in0 (new since v15.20, contains the workspace settings).
Start now UltraEdit which will create both files new with the default settings. Test your problem with opening a file by double click.
If UltraEdit window comes to foreground, the problem is somewhere in the INI file. Open uedit32_bak.ini and delete all groups named [ToolBarState1...] which contain workspace settings of the previous GUI not available anymore. Delete also all groups named [TBCFG...] and [...-SCBar-number].
Save the cleaned INI file, close UltraEdit and copy uedit32_bak.in0 over uedit32.in0 and uedit32_bak.ini over uedit32.ini. Start UltraEdit, open Advanced - Configuration - Toolbars / Menus - Miscellaneous and press the button Clear History. Close the configuration dialog with button Cancel. From time to time the histories should be cleared to reduce the size of the INI file. Close UltraEdit (for clearing the histories in the INI) and restart it.
Now test again if the problem with the flashing button instead of bringing the UltraEdit window to foreground still exists with your settings and with a cleaned INI file. The reason is that Windows does not bring a window to foreground when the application needs too long to respond. Instead Windows flashes just the taskbar button to tell the user to activate it.
Extra hint: Advanced - Configuration - File Handling - File Change Detection contains some settings which can improve perfomance (and save battery life time). You can disable the file change detection completely or what I prefer, have it enabled, but enabled is also the setting Check files for changes only on application focus change. With that option enabled the file change detection is not running as a background thread reading and comparing the file information of opened files every 5 (?) seconds. Your problem could be that this background thread has detected a file change of one of the opened files while another application has the focus and therefore when UltraEdit gets back the focus, it displays first the message, if you want to reload the file or not. This message box could be the reason why the UltraEdit window does not come to foreground when you open a file by double click. With disabling file change detection in the background, this problem does not exist.
Best regards from Austria