I have three workstations with the same motherboards, all identical (same revision, chips, etc.). Motherboards have a Winbond W25Q128 flash chip.
 
I have flashed two of those successfully several times with Buspirate (internal programmer is a no-go on these boards).
 
On the third motherboard flashrom fails to identify the flash chip 8 out of 10 times and terminates. Then on the few occasions when it does identify the flash chip it fails to complete the flashing process successfully (errors erasing).
 
I have tried two different Buspirate flashed with firmware 5.1, 6.0, 6.1, and 6.2 (same results regardless of firmware). All the hardware connections are fine - I have checked continuity from the flash chip legs to the Pomona clip to Buspirate. My wire leads from Buspirate to the Pomona clip are short, 10 cm. I am certain this is not a hardware issue since Buspirate/flashrom work on two other motherboards.
 
I just do not know what other test should be pursued to get to a resolution. I have attached the –V logs for a successful  flash from one of the two boards flashrom works,  log where flash chip found but aborts on errors, log where flash chip  not found, and a –VVV log for the latter. I note that the ‘probing’ results are very different but do not know what that may lead to conclude.
 
Any pointers, comments, help welcome.