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One thing to check on HM Physical appliances when they are abnormally slow with no explainable reason is to make sure the device has appropriate cooling. If the CPU cooling fan fails, the device will drop the CPU down to 1/2 of it's normal power for heat dissipation, causing the box to run extremely slow.
Two ways to check this: 1) With a phsyical RS-232 console hooked to the box, reboot the appliance and see if there are errors displayed that will clearly show cooling fan fail on the CPU, and it's throttling.
2) You can also check under the HiveManager Web UI, under HOME--->LOGS--> System logs, to see if it reflects the same.