I get that too with icd3 and pk3 , I think it may be a usb issue unplugging and reconnecting programmer fixes it for a while.
saleae logic8 now does it too [keeps saying it can't keep up even @50k s/sec it used to do 16million] . perhaps my i5 laptop just does not keep pace with the real world any more now its bogged down in windoze 10