I think I have worked it out

.
If you interchange tube lines you do not have to tap out at the interchange, only at the end of your journey, you are charged 1 fare.
If you interchange the EL on your journey, you must tap out at the station you alight from, tap in to the EL and out when you alight and you are charged 2 fares, one for the existing network and one for use of the EL.
If you do not tap out of the existing network, even though you can use the same card for both, you are charged the maximum daily fare as you are not recorded as leaving the existing network.
As this has not been publicised and there are no signs to alert you to this, you are only aware if you check the amount you are paid for your journey. The EL requires you to tap in at every interchange, and out again to leave it, but there is nothing to tell you that you need to tap out of the connecting train you used to interchange if you have used one.
Using the same card to tap into the EL, does not record you as leaving the existing network and leaves you liable to extra cost. They are ran as separate networks with separate charges in the same way the Thames Clipper is.
That is my understanding of the situation from some quick research and what I was told.
No wonder my friend said the DLR from Woolwich has seen no change in passenger numbers,
