Are there any errors showing up in the console?
Edit: What it likely is is that the base is flagged as an "NPC" base I'm guessing because its been copy/pasted. As of the latest update, Raid Protection will ignore bases that are spawned in (by Raidable Bases for example). It gets flagged as that if the building blocks of the base do not have an "Owner" associated with them. You can use a plugin like admin hammer to see who the owner of a block is, and I believe you may be able to set ownership through that plugin as well.
Ideally, the fix for this I believe is that the copy/paste plugin should be setting the paster as the owner for all the building blocks.