This problem is related to the problem that SuRun interferes elevation of all windows processes, not only those started with SuRun. (I pointed this out in a previous thread in this forum.)
I use a file-manager (FarManager,
https://www.farmanager.com/) that allows elevation of its own rights when copying files to a folder that needs it (e.g. to "Program Files"). It does that by creating a sub-process with elevated rights. The sub-process is invisible (it does not have its own window), and its parent process is normally the file-manager process.
After installing SuRun, it doesn't work this way anymore. When the file-manager wants to elevate itself, the secure desktop occurs as usual, but now with the SuRun dialog instead of the standard Windows one. The result is that the elevated file-manager process is now visible and its parent is not the original file-manager process.
Windows 7 Pro x64, SuRun 1.2.1.2.