Balloons are typically filtered out because they exhibit unusual characteristics (primarily they tend to move really slowly). Our flight tracking engine has complex rules for determining what is and is not considered a trackable "flight to make sense of all received data from all of our many data sources, including Mode S/ADS-B. (Also, make sure you have “position-only” tracking enable in your FlightAware.com account since these flights are typically not a schedule or flight plan.) We are working on additional improvements to enable better tracking of position-only flights and will have more announcements about that in the future.
My PiAware systems are currently tracking HBAL187, 60,500 feet at a mighty 12 knots over Northern California’s Wine Country. Must be quite a view from there.