I'm not sure if it's related to the issue you're having, but if the PCM is waiting to write to it's own flash for any reason (after a CKP relearn for example), it will not allow you to write to the flash until after it writes it own data. I can't remember if it will keep you from reading or not. To get it to write it's data and be ready again, you have to turn the ignition off with battery power connected and wait. 30 seconds might be enough, but I wait 1 minute. This can be an issue particularly with bench harnesses that don't have an ignition switch or an incorrectly modified stock harness. Just something to be aware of. Always double check battery voltage and make sure headlights and other unnecessary loads are off if flashing in the vehicle.