Whole Wheat Sourdough didn't rise 3rd time

I'm pretty new to bread baking.  I've done lots of reading which I find interesting and have baked a few white flour loaves.  They turned out fine.  I baked the whole wheat sourdough recipe from Laurel's Kitchen yesterday and encountered a problem.  This recipe is entirely whole wheat except for the sourdough starter. The first two rises were fine, but the third rise, in the pan, was a flop.  It rose maybe 50% in 4 hours!  I did bake it and it tasted fine.  I'm wondering if the yeast got too hot during the third rise.  With all rises I put it in the oven after turning the oven on and off for 30 secs.  The 3rd rising period was in the oven for 30 minutes and on a heating pad for the other 3+ hours!  I had the pad on low at first and then bumped it up after an hour or so.  I had a towel on the pad and a plastic container over the top of the bread. 

Her recipe states the 3rd rise will take half as long as the 2nd which would have been about an hour.  I would have expected to see some rising within 30 minutes which I barely saw. 

What most perpexes me is that if it rose fine the first two times why not the 3rd, unless as I said, maybe I got it too warm.

Thanks

Ginny