Can't offer any explanation (the more science investigates lightning, the more questions get raised!). But anyone who has lived in the Kimberley region of NW Australia will be familiar with the phenomena. The TS there produce some truely spectacular effects.
The thunder you describe was common during the dying phases of a cell. As the cell decays to mostly a midlevel stratiform type of cloud, the lightning strokes would run inter cloud tru this stratiform. The resulting thunder would roll on seemingly for ever, an extremely deep resonous type that shook the very foundations of our house. The thunder didn't seem to stop, instead only decreasing as it sounded to get so far away. Awesome stuff, best experienced from the ground, they were fearsome to aviate around!!!!