When the underground belt ends are dropped by the bots, they are frequently in the wrong orientation. I suspect that what happens is that whichever end is dropped first becomes the 'input', and the second end then becomes the output. This is partly because the wrong orientation I was seeing was frequently facing away from my base.
At first I thought I'd made a mistake in belt placement, so I had bots pick it all up, then I tried again paying careful attention. Nope, I still frequently got reverse belts.
Another idea is that maybe belts take their cue as to direction from the orientation of the belts around them, and so when I tile a whole bunch end-to-end across the landscape, that messes things up. That would explain why long stretches seemed to end up with the wrong orientation.
Here's the blueprint string for my belt:
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0eNqVkE0KwjAQRq9SvnWEttYucgdPICKtDhJIJyVJ1VJ6d6etiPizcBXmy+S9zAyobUetNxyhB5ij4wC9GxDMmSs7ZbFvCRomUgMFrpqp6vhE/uydnKuabMSoYCS7QWfjXoE4mmhoYc1Ff+CuqclLw2+KQuuCPHQ8mQW2Wiv00KngT8bTcbnK1fNX3HaT/EOS/yHJvznKd4dMNe9Av6xMwVbClGxb3ZJg3TWZdclDdCEfFlpR5OWmyNJNOY531oZ8zw==