Ahh, yeah, ports B and C on the 68230 connect to an MSM58321 clock chip, which also provides the TIN timing source. So this isn't a 68230 defect at all (Or at least right now it's not).
the timing source isn't obvious from the schematic. it's from a Seiko SPG8651 (U1), which is why the data sheet is in the directory. They have it jumpered for 100Hz
(Or at least right now it's not).
