I'm just guessing at the cause, but it could be explained by at what point in the render process the software you're using is taking its frame-rate reading.
For example, in a true triple buffering design, the GPU is permitted to render as fast as it can and if you add Vsync, the output will be synchronised to the display. The GPU renders to two back buffers, either of which can be flipped to the front buffer for display. If a completed frame is not needed by the display, then it's dropped from one of the back buffers. This way the display gets its 60Hz update and the GPU can churn out frames as fast as possible.
If windowed borderless mode uses a technique like this and if your frame-rate counter is taking its reading from the back buffer, then it'll display >60fps at times, while the out put is actually synced to 60Hz. For this theory to be correct, it would mean Aero desktop display uses true triple buffering + vsync, so who knows?