Josh:
A normally-operating S4 in program 3 will give impulses on 18 channels - #0 to #17.
On the back of the S4, you've got banana sockets for c0, c3, c6, and c9. Your question deals with c0, c1, c3, and c4. This leads me to believe you've either got a port extender, such as the MC-18 or OC-18, attached to your S4's DB25, or you've got a DIN cable(s) attached to one or more of the PHOTOCELL DIN sockets (A, B C).
Since your problem is replicated exactly on the two S4s, this leads me to believe you've got a problem with your DIN cable or port extender.
The S4 is an astonishingly reliable device, hence the chances of two S4s developing the exact same problem at the same time is nil.
I would look at whatever cable or device you're using to access the channels.
Detach everything from both S4s and short the c0 c3 c6 and c9 bananas on the back, one at a time, with a paper clip. If you get impulses from all the channels on both S4s, then you've got your answer.
A few weeks ago my OC-18 died, which made my S4 exhibit problems similar to what you are experiencing. A few channels died, then more died, until finally none of the channels worked. I detached the OC-18 and did some tests using the S4's onboard banana jacks and the DB25. Everything on the S4 tested OK, and sure enough, the problem was the OC-18.
I had never seen an OC-18 fail before, and neither had Fred. I've actually never seen an S4 fail either, other than EXTREME pilot error - such as users installing alkaline bateries into S4s set up for NiCads (batteries explode), or somebody plugging 120v into the horn port.