Actually turns out I had clip low turned off, and if that's turned on and set to 0 it integrates ok. It's not immediately obvious to me if I should have clip low turned on, if in principle my bias could have pixels with 0 value legitimately. I'm not familiar enough with the workings of a DSLR CMOS.
It's odd that the integration seems to succeed on OS X though, but not Ubuntu if it is set without clip low.