Below is a stripped down version of the permissions file. When I am a member of Moderators, I get notifications. When I make my self a member of Admins, I cease receiving notifications.

In both cases issuing the following command...

/pex user <me> check preciousstones.alert.notify.place

...returns true.

============== Permissions.yml ================

Moderators:
prefix: '&0[&1Mod&0]&7 '
options:
rank: '60'
rank-ladder: Staff
permissions:
- preciousstones.bypass.allowed-only-inside
- preciousstones.bypass.allowed-only-outside
- preciousstones.bypass.commandblacklist
- preciousstones.bypass.damage
- preciousstones.bypass.entity-interact
- preciousstones.bypass.entry
- preciousstones.bypass.hiding
- preciousstones.bypass.mine
- preciousstones.bypass.no-allowing
- preciousstones.bypass.teleport
- preciousstones.bypass.toggle
- preciousstones.manual.bypass.potions
- preciousstones.alert.notify.(place|destroy|bypass-place|bypass-destroy)
- preciousstones.alert.warn.(entry|fire|pvp)
- preciousstones.alert.warn.(use|place|destroy|noplace|destroyarea)
- preciousstones.alert.warn.(conflict|unprotectable)
Admins:
prefix: '&0[&cAdmin&0]&7 '
options:
rank: '30'
rank-ladder: Staff
permissions:
- preciousstones.benefit.disable
- preciousstones.admin.isadmin
- preciousstones.admin.insert
- preciousstones.admin.(counts|list|locations|mark|visualize)
- preciousstones.admin.(allowed|setowner)
- preciousstones.admin.undo
- preciousstones.admin.delete
- preciousstones.admin.reload
- preciousstones.admin.fields
- preciousstones.admin.clean
- preciousstones.admin.revert
- preciousstones.admin.details
- preciousstones.admin.bypass.potions
- preciousstones.admin.viewconflicting
- preciousstones.bypass.destroy
- preciousstones.bypass.entryalert
- preciousstones.bypass.item-frame-take
- preciousstones.bypass.limits
- preciousstones.bypass.place
- preciousstones.bypass.protection
- preciousstones.bypass.purchase
- preciousstones.bypass.setradius
- preciousstones.bypass.unbreakable
- preciousstones.bypass.use
inheritance:
- Moderators

Turn this off on the config: disable-alerts-for-admins: true

I apologize. I logged in and didn't see this issue in the issues list, so I thought I previewed and forgot to submit. I have submitted a second one mistakenly. I'll attempt to remove it. I will also try your suggestion and let you know whether it worked or not.