I erroneously posted earlier this had to do with how much rep you invested.
It is completely random. BUT ... I would encourage you to EMBRACE the hour with the short cool down.
I love being able to hop planets whenever I want because the perk only lasts an hour and then resets quickly. I love repairing the dekas and knowing that I can do it again shortly.
It does suck if you want to invest some credits into providing more Contra, then it is not worth it, but it is great for some of the more immediate needs.
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