Arria 10 Passive Serial Configuration Error

We have two PCB designs with Arria 10 FPGAs on then and in both designs we are able to program the devices using the byte blaster 2 cable over JTAG, but on both boards programming over passive serial fails after sending 240000 bytes. We see this problem with our own configuration firmware and using the byte blaster 2 cable with Quartus prime. We have triple checked the design and layout and we have confirmed the clk and DATA0 have the correct RBF data at the start, so there are no spurious bits etc. MSEL bits are set to 1 per the a10 config guide. The problem happens on multiple boards so it isn't likely a bad chip/manufacturing problem.

We are out of ideas, so any suggestions on things to look up gratefully accepted..

Thanks,

Andy.