Whenever I saw low productivity, I would try to diagnose the cause. Not only that, I would also ask myself the question, "Is the low productivity within my power to control?" Most of the time it was within my power to control. Occasionally, not. I've never been a fan of the flat-rate system, although that's the main tool I use to measure productivity or the lack thereof.
Ironically, the majority of the time, I would cure the problem with an adjustment that's made on the front counter and not out in the shop. What I was able to do was done with changes I made to more accurately written estimates and invoices. Because we were a transmission repair shop, we billed by the job and not by the hour, although we used time as a common reference point. Our estimates and invoices never had the number of hours or how much an hour it was for any particular job.
Using that method of billing made it easier for both my techs and myself. Of course, I wouldn't start billing with reckless abandon for fear of pricing ourselves out of the market. I understand that most shops do have an hourly labor rate and bill by the hour. I'm not saying to follow my method because it's not for everybody and every shop. Customers usually have some vague idea as to how long a job takes and how many hours sounds reasonable. Major transmission repair work is not that way in the eyes of the customer. They have no idea and generally just look at the bottom line, including sales tax. Our customers had a written estimate upfront, so there were no surprises. 99% of the time, our estimates were written in stone. Because of this, we rarely had price objections.