I can confirm the exact same thing here.

Kubuntu 15.04
intel-microcode 3.20150121.1
CPU Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz

When intel-microcode is installed the CPU frequencies are stuck between
400 and 500 Mhz, they just slightly scale between this two values. No
special messages in dmesg as far as I can tell.

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https://bugs.launchpad.net/bugs/1480349

Title:
  Breaks frequency scaling in Xeon® E5-2687W v3

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