W48C60 is just the CPU clock. The CMOS and Clock is in the NS PC87306 Super I/O chip AFAIK, the 82371SB does not have a CMOS/clock like 82371AB/EB. According to 87306 datasheet pin 7 is Vbat for the Clock and CMOS keep alive and it says this about it:
Real-Time Clock: DS1287, MC146818 and PC87911 compatible, 242 Bytes battery backed-up CMOS RAM in two banks. Separate battery pin, 2.4V operation. During system operation, power from the system is used.
When system voltage falls below battery voltage, the Power Management function switches the RTC cell to battery power.

Does it keep time when power is off for a while with a battery in the coin cell ? If it does you have some sort of CMOS issue in the chip. Sorry cannot think of anything else.

that intel zappa has seen better days. the PCI slots are yellowed, and the board itself is pretty dirty and the SMD caps may be leaking since these are like those SMD caps that i usually have seen leaking on old Macintoshes and Amigas.

I remember this being a common problem on Intel's own Socket 5 motherboards. Zappa, Zappa/E and Morrison boards.
All the boards use the PC87306 Super I/O chip. The CMOS will not save settings and won't keep time with power off.
It isn't a bios issue because I remeber flashing various MR-BIOS versions and they worked great but didn't fix the cmos not retaining settings.
PS. Be VERY careful using a multimeter reading pin 7 on the I/O chip with the battery in. You will need to isolate pins 5-6 and 8-9 either side or will short the chip. The gaps are tiny.