If permanent look for access-list issues and access-group on vty lines.
If it is intermittent look at routing table when the problem is there and when it is not.
Also recommend using a loopback interface to access the router so the router can be accessed whenever at least an interface is up.
Finally you mentioned NAT. If an intermittent problem is present NAT and route flapping might as well be a problem (if a NAT entry is present and routing changes, you might end up with nasty surprises).
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