I still experience the issue mentioned in my original post. However, I deal with it by manually setting the print options every morning, after turning on Profile. 

Today I also went through this routine, yet I noticed that the print options reverted TWICE during the day, even though my computer was always on (and I did not even close Profile). So, some clients got their copies with double-sided pages flipped on short edge.

I'd love to hear from Profile's support here--is there ANY solution to this issue???