There are many things this could result from. Obviously your assessing physiotherapist would have checked to see if the origin of your pain was from your lower back. If it is just a muscular problem, correct strengthening of the hamstring muscles (especially an eccentric strengthening programme) is extremely important. Also, strengthening of the stabilising muscles of your lower back and hip region is important too. If your hips and core are not strong, your hamstrings sometimes have to work overtime to do the stabilising for them.
Once your hamstrings are stronger, it is important to reintroduce fast contractions of the muscles to prepare them to be able to cope with speed on the pitch.
If you are still having pain jogging, I assume your initial hamstring injury was fairly severe? Gentle stretching of the hamstrings, glutes and surrounding hip muscles is important.
Perhaps another visit to your physio is in order.