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You don't mention what instance types you're using. If you're using the T-series instances then it's possible that you're running out of CPU credits. Even though the operating system is showing low CPU usage it may still be throttled. Check CloudWatch Metrics for those instances and see what the CPU Credit metric displays.
If that is the problem: To fix it, either change the instance to "Unlimited" (but you'll be charged 50 cents per hour if the CPU credits are exhausted); choose a larger instance size; or choose a different (non-T) instance type.
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