Cannot remove silence from a long video

Ran into the same issue. Anything over right about 48 mins would look like it was about to shorten hugh chunks of audio. Anything under ~48, same settings, it would show the silence it was going to shorten correctly. In a support session with Adobe, they tested and even though it wasn't showing it the same, it did indeed remove the audio correctly from the whole file, you just couldn't check the individual shortens. I've switched to just adding a marker at every 30 mins make (to be safe, could probably be 48 mins or thereabouts), calling each one "s1, s2, etc" and then just highlighting the 30 min section and removing the audio from each one individually. You should test to see if the full audio scan actually removes the correct silence and it may just be showing it incorrectly like mine. 

There isn't a limit that I'm aware of, and it works fine here with a one hour file - but you need to be absolutely sure that the 'define audio' settings haven't changed, especially the 'for more than' setting. This can make a massive difference to the results you get. In my experience you often need to experiment with the scan settings quite a bit before you get the results you want.