Not sure what it is, but that's been one of the steps I use to try to troubleshoot problems on my own computer. After verifying that, then I try to look at everything at a user level that might be different (Library folders, application support, etc.) Some have had success with deleting Keynote preferences, but without having more of an idea what's wrong, I'm not sure that would be a solution for you (especially since it "appears" to be a system level problem that's alleviated by this user level change).
I just shut down Keynote. Then, I double-clicked on your file you provided. After opening, I click on slide one then click to play. I'm not even getting a 5 second delay. When I play I immediately see the first screen and there may be a delay of half a second or so after I click for the transition to the slide with the chart to begin. Does this other user also show improved performance if you turn off the Scaling feature?