Thinking my first clip+ might be defective, I picked up a second one to test. Here’s the results:
1000hz
Dell D630c (laptop) - plays 1000.02hz
Sansa E200 - plays 1000.39hz
Rio Karma - plays 1000.48hz
1st Sansa Clip+ - plays 1002.47hz
2nd Sansa Clip+ - plays 1002.47hz
That gives both Sansa Clip+'s a pitch error of 0.247%, compared to the next player (Rio Karma) at 0.048%.
From this I can say that this pitch bug is real, and can and should be fixed via firmware. I don’t think it’s too much to ask for Sansa to at least equal the sound quality performance of their previous generation player, the Sansa E200.