One thing to check - does your top off tank sit higher than the sump it is being oumped into? If it does, the ATO can turn off the pump, but you could still have more water siphon into the sump until the levels equalize. If the height difference is small, you might not notice what is going on right away.
I had this happen when I switched to a larger container for a vacation and the container had to sit outside of the cabinet and I made the mistake if setting it on a stool rather than directly on the hardwood floor. This meant that when the container was full, the first tie the ATO kicked on, it filled, the pump turned off, then it continued to siphon a few more quarts. So it didn't make a big problem, but was enough to trigger the high water alarm on my ATO.
