Nevermind. I was able to get them to show up by selecting the missing columns from the Columns dropdown.
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My bet is the issue is with 'UI customization'.
Anytime you make changes to a grid.. whether that be a link control grid, saved search grid, default grid, etc, those changes are entered into the system.ui_component_state table. Changes can be a subtle as simply making a column wider.
The moment you have an entry in this table, any administrative changes that are made dont apply to you anymore.
This is where it can cause issues, like yours, perhaps, and others, such as changing a console, or view, and the users not seeing the change.
Here's a snippet of that the table looks like:
Best way to get started... Filter based on your app_user_id. You can find your app_user_id by going to the system.app_user table. Then look at the state_key column.. in your case you're looking for a 'link-control' entry.
You can blow away entries in this table. Changes will show in FootPrints immediately (reload the item in question, such as open the form..) no need for a Tomcat restart. Removing an entry from this table removes the changes the user made to the area in question (link control, avanced search, etc) and returns it to as it is configured by the administrator.