The problem you are experiencing migth be common mode noise present on the batteries. The optocouplers have a bit of capacitance from input to output, which will couple the noise from the switcher through the circuit. I would do what sensacell suggests, especially the schmitt trigger and lower value pullup. Also some HF filtering on the inputs might help. And I would change all the ICs before you try again.

 

Yes

So you put 0.1uF ceramic bypass capacitors from every IC power pin directly to ground with as short a lead as possible?

 

I have experienced problems with opto-couplers in the past when I wrongly assumed that they truly isolated things perfectly.
There is always some capacitance between input and output in any isolator, this combined with a 10K pullup and a slow 4N35 coupler means that the signal spends a long time in a vulnerable meta state where this minute capacitance can couple enough signal in to cause multiple transitions.

A lower value pull up would help.
A faster coupler would help.
A lower capacitance coupler would help.
A schmitt trigger input would help.

I think this is my problem. I believe the primary and secondary are capacitively coupled. Perhaps the biasing of the battery stack is creating voltages across the optocopler.

 

The problem you are experiencing migth be common mode noise present on the batteries. The optocouplers have a bit of capacitance from input to output, which will couple the noise from the switcher through the circuit. I would do what sensacell suggests, especially the schmitt trigger and lower value pullup. Also some HF filtering on the inputs might help. And I would change all the ICs before you try again.

I tried a lower pull up it worked well. The transition time was quicker which meant it spent less time in an undefined region.

 

It's false economy to omit bypass caps in a circuit like this.
As others have said, it's the impedance at high frequencies that counts, even at slow clock frequencies, the pulse edges contain very high frequency spectra.
A board full of flip flops is aching to misbehave without bypass caps.

I looked for that. I probed directly to every Vdd and Vss pin. I saw no difference with or without a capacitor over the same Vss and Vdd.

 

You need a bypass capacitor. You see your ICs are failing right?
You need a Z-Diode too with 18 volts.

The ICs stopped failing after I decreased the current driving the optos LEDs and I changed the resistor network to discrete resistors. I believe I was overtaxing the CMOS chips by making them drive 15ma into a LED and the resistor network insulation was breaking down. My last problem was clock jitter. I tried caps to stop it, but it was ineffective. I really wanted the caps to work too since the only other solution was increasing the current through the optocouplers, which I don't believe the CMOS inverter can handle.

 

What caps did you try to fix the clock? Slowing the edges rarely ever works, usually just makes things worse. Try adding as schmitt trigger on the clock right after the optocoupler.

 

I looked for that. I probed directly to every Vdd and Vss pin. I saw no difference with or without a capacitor over the same Vss and Vdd.

The kind of nasty glitches that the bypass capacitors fix are almost impossible to catch on a scope, that is why I always put them in- needed or not...