How to prevent eggplant having a tough or rubbery texture
Make sure your initial cooking is reasonably fast and hot, and from there just cook it until it's soft enough for your tastes.

Many vegetables firm up when cooked at lower temperatures, especially in the presence of salt. From On Food and Cooking:


  It turns out that in certain vegetables and fruits - including potatoes, sweet potatoes, beets, carrots, beans, cauliflower, tomatoes, cherries, apples - the usual softening during cooking can be reduced by a low-temperature precooking step. If preheated to 130-140F/55-60C for 20-30 minutes, these foods develop a persistent firmness that survives prolonged final cooking. ... Firm-able vegetables and fruits have an enzyme in their cell walls that becomes activated at around 50C (and inactivated above 70C), and alters the cell-wall pectins so that they're more easily cross-linked by calcium ions. At the same time, calcium ions are being released as the cell contents leak through damaged membranes, and they cross-link the pectin so that it will be much more resistant to removal or breakdown at boiling temperatures.


Eggplant isn't on that list, but I believe the enzyme in question is pectinesterase and is present to some degree in many vegetables, and I've had eggplant that stayed fairly tough through longer cooking, so I suspect it's a possibility here.