The spaces directory only lists the spaces you have "can use" rights in.
Your admin privileges include the ability to see all spaces in the admin pages, and update the permissions in there, but it does not give you a blanket "can see everything because I'm an admin" right (it's a bad permission model and one that Atlassian stays away from)
You need to be careful with that case.
If the problem was "I don't see them immediately", then that's because it takes a few minutes to catch up. Do not re-index manually, leave it for a few minutes.
If the problem was "I don't see them after the system has had time to index it all", then you have another problem - your system is being broken by something that stops the indexing from working properly. You really need to investigate that and fix it.
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