Alright, I got to the bottom of it. There was a bug with how very fast tasks were being timed, which is now fixed. The issue you were seeing above wasn't related, it's a math thing.
The speed a task is done at isn't linear, it's exponential based on the skill level. That means that the first 10/25/50% of the task takes a lot longer than the last 10/25/50%, because your level went up while doing it.
Taking off 10% of the work to be done can be thought of as taking it off of the end, when the task is being done the fastest. That explains why there isn't a 1:1 conversion of work required:time taken.
Either way, it's still worth it to build keystones. Thanks for pointing it out, I got to bust out the old Excel sheets!