I had some teleport-on-sneak stones set up and working, and without changing my config, later stones did not work.

ps info shows everything expected, welcome messages trigger, names are confirmed none or the same set value, though it was stating that the fields were 1x1x1 even though the welcome triggered fine.

Strangely, restarting doesn't even seem to help. I'll start from scratch to see if I can figure out what's busted.

Figured it out!

preciousstones.bypass.teleport applies even in cases where teleportation is not to remove someone from somewhere or anything like that.

I think you either need to change your doc, or make the permissions node apply different to "teleport-on-sneak" or even make different flags. I'd say make the bypass only apply in such a way to fields with "applies to: not allowed" for "applies to: allowed" the bypass flag shouldn't keep an admin or whomever has it from voluntarily teleporting.