Now that I have the full version, with more sounds to experiment with, I have found out why you called the 'Ooh Baby' artifacts 'subtle'. My best-loved example is voices / Basses Ohs f. If you put this on stretch and press & hold F0 (which is a root key!), you will hear a rhytmic distortion which is much louder than the sound itself. It seems to me that the distorition (call it 'artifact' if you want, but I think that expression does not fit the situation) occurs at the loop point.
I'm not so sure whether it's still ok not to call this a bug... but I think that if you can get rid of this effect, then the other major artifact problems will disappear, too. And that would be great! The basic stretch sound is very good, it's just those distortions which render it useless for many sounds.
Perhaps it's bit bold to suggest something this simple, but have you ever contemplated running the original signal (including loop points) through something like a 15kHz low-pass filter before you do the actual stretch operations?
malamut