Question: What's the difference? Why is one number way off?
They're both calculated differently.
The number at the bottom is calculated from the data on screen. The value will depend on your zoom, the number of visible waves, the noise on those waves, etc. This is usually the preferred number, although you always need to bear in mind what's visible on screen (eg. it won't work at all if there's only half a wave visible).
The number at the top comes from the trigger circuit. It counts the number of times the trigger was fired per second. If there's noise on the signal you might get extra counts as it wobbles past the trigger voltage level. This is why turning on the bandwidth limiter can help - it's a low pass filter on the input and can help a lot with the accuracy of measurements when you're looking at low frequency signals.
Note: Neither of these methods is guaranteed to be 100% accurate in
all circumstances. That's oscilloscopes for you.
(Note to Bud: this is true of
all oscilloscope, not just this one).
You can also take measurements manually. Capture a single wave on screen with as much zoom as possible. Turn on cursor mode. Move the cursors to the start and end of the wave you just captured.
I see a square wave on the count, so I wonder if that has anything to do with anything?
That's just a graphic, nothing to do with anything.