When I have used saponin, it is used from the first rinse, through ALL
steps until chromogen.  The last rinse is just PBS without saponin
BEFORE chromogen development.  Idea is to keep the membrane open
for reagents, antibodies, etc to penetrate to cell interior, and then
reverse the effects of saponin permeabilization, close up the membrane,
develop the color.

It might be advisable to ask supplier of kit, if you need to do this
throughout the TUNEL whole procedure.
My protocol is for staining cytokines attached to Golgi, with
some different parameters (???) than you TUNEL method.

Hope this helps,

Gayle Callis