I have two other suggestions that may help.
We found that with TestStand 3.1, that we also had to add a checkmark to the option:
Configure menu
Model Options
Check the "Discard Results..." box.
We also use the "On-the-fly" reporting running anywhere from 2000 to 50000 thousand steps for a test. As the test progresses, it would slow down.
Lastly, very early on, I discovered that with the "Tracing" enabled, in the "Configure" menu, Station Options, that the slider for the speed was not set to "Fast". This may also have a bearing on how fast each step executes.
Mike