Then apparently, HDDScan is using a spin down command which puts the drive into a state where it doesn't wake up on the next command (which is not what we do). Given that sending a spin down command to the drive directly, inherently doesn't inform the OS, this is actually dangerous, as the OS can try to send a critical command to the drive and error out (such as saving transactional file system metadata). Although, it should retry the failure a number of times.
As for Scanner vs. smartctl (I presume they're sending the same command as us, but haven't looked at their code), there might be something wrong with the Scanner's stand by in general. I think something may be broken in the latest BETA (and I'm not how far back it goes.
I'm going to look into this soon.