Avoid re-setting Save As and Save In window sizes and positions

I often reset the size and position of "Save As" or "Save In" windows by dragging them to the desired size and position, then closing them by clicking the X while holding down CTRL. This works fine ... they reappear in the reassigned position and size each time I see them ... until I run CCleaner. I have tried unchecking the Window Size/Location Cache, and in fact have unchecked all the Windows Advanced options, but that didn't help. Can you tell me what CCleaner is changing that causes my positioning to be lost, and if there is any way to tell CCleaner to skip that change?

What program are you using that causes this?

As a test:

I've just changed the "Save As" screen size in Notepad. It will constantly remember the size I changed it to while Notepad remains running, also if I run and clean with CCleaner while Notepad is open Notepad still remembers the size. However when I close Notepad and re-open it to "Save As" again the size is completely forgotten.