What breed? PSSM1 can start to show up as discomfort as a work session progresses.
Hopefully the grinding towards the end of 40 minutes simply means she’s tired and getting tense. It’s hard to know what real base of fitness she has, but it may simply not be enough for the work being asked.
I’d back off to 30 minutes for a few weeks and see what happens. Very correct work from the minute you get on, and that might mean simply asking her to march along at the walk for 10 minutes to loosen up and start getting her back swinging, so “correct” there means no slugging along.
Last 5-10 minutes is more free walking. The middle 10 -15 minutes is more concentrated work suitable for her level of fitness and education.
See how that goes, and if she stops grinding, then gradually increase the middle work time, always increasing time OR intensity but not both in the same ride