I was trying to change the format of the generated link so I added --format '%T/%T-%S %m%-%d%-%y' to the end of commands in /etc/cron.hourly/pretty. If I run that file directly, I get the expected result, but after a while everything reverts to the default.

So if that isn't generating the symlinks, what is?

Thanks.

Tuns out, when I edited /etc/cron.hourly/pretty, it created a pretty~ file that was a copy of the original and was still executable. I'm guessing it ran my modified pretty, then ran pretty~ and restored it all to default. Deleting it made everything work fine.

That sounds about right, anything in those cron dir will be run regardless of it's a backup file or not.