Your problem is likely a hardware or wiring problem.
By elimination, I would try those tests whith S4 only (no software):
-whith 2 short wires pluged in banana jacks c0, can I generate a start pulse by
manualy shorting them?
-same thing with c3 and c6? If so, the problem is in the hardwire of the mountain.
Do the "line test", like described on parag. 2.5 in the ALGE manual.
If not, it's a defect of the timer. Not a setup problem.
-likely as above, short the "A" photocell jack by using pins no. 2 (bottom right)
and 3 (bottom), with 2 little wires manualy. It should generate a stop pulse and
you should hear it. Do the same with "B" and "C" jacks. If not, it's a defect again.
If you got a signal from each jack, it's a cable problem from the photocell, or
the photocell itself.
But in fact, it's difficult to conclude that you had 2 cable problems at the same time
when using timer (start AND stop).
With the result of those tests, I would suggest others.
Doc.