There is a similar thread
in a german message board about the snesCIC and the PIC 12F629.
I had the issue that a SFC with several different snesCIC/PIC12F629s would boot everything but SA1 games and only after replacing it with a superCIC/PIC16F630 the SA1 booted fine while the same snesCIC/PIC12F629 would perfectly read SA-1 games in my SNES cartridge reader
Interestingly the SFC died shortly after so it could be an edge case where a broken SNES only works with certain chips. I did buy a second SFC to clarify but that one already arrived dead from Japan.
Your case is even more interesting since you are using the same code on equal PICs. So it's not just a slight difference between the superCIC and the snesCIC but it can also happen with two superCICs.
Which again leads me to believe that it might be either the fault of a particular picky SNES console or of bad quality control by the PIC manufacturer.
Do you by any chance have a second SNES that you could mod?
I also believe that the CIC in the console could run at slightly different speeds in different consoles since some have a dedicated 4Mhz crystal for the CIC while newer console use a clocksignal from the audio chip, I think. Just speculation though, haven't done any tests.