Well, I ordered 3 new ones and some new watch crystals which arrived the other day and I measured the x1 & x2 pins and they also measured ~39pf, so, I guess by measuring between the x1 & x2 pins is inconclusive. The new watch crystals had a static capacitance of ~1pf, which was as per the datasheet, wheras the ebay ones measured ~2.3pf the
So next would be to verify all the registers are working and to leave it running on battery backup for a few days to see how it runs, using a combination of the suspect chips with the ebay crystals and then the new crystals; then try the new rtc's with the ebay crystals, and then the new crystals; if that doesn't work then I'll have to start looking at bad pcb, noise etc.