Digitrax auto-reversing units such as the PM42 or AR1 require a "hard" short for them to work properly, which means there must be good current flow to both sides of the gaps, on the reversing section side and on the "normal" side. For this reason it is poor practice to put the gaps immediately behind a turnout relying on the points of the turnout to supply the current to the "normal" side of the gaps leading to the reversing section. Resistance through those points often reduces the current to where a good short cannot occur preventing the auto-reversing unit from being able to do its job.
Also, on long reversing sections too few track feeds from the auto-reversing unit can cause the same problem on that side of the gaps. Relying on current through the track itself, particularly rail joiners, is not wise as rail joiners are notorious for being poor conductors of current.
One of the biggest mistakes is in the gaps themselves. The wheels of the rolling stock Must be able to make contact with both sides of the gaps simultaneously to create the necessary short to activate the phase change in the auto-reverser. This means you cannot have insulated rail joiners in the gaps on each end of the auto-reversing section that come above the rail or even level with the top of the rail as no short can occur.
Make sure that the Reversing Section itself is powered only by the AR1 and not from any other source.