Just want to chime in here.  I have this problem as well.  I have had it
on several motherboards, several CPUs, and every version of Ubuntu and
Debian I have had.  I am currently on Lubuntu 16.04 with kernel 4.4.0-78
and this issue persists.

My CPU has a stock speed of 3166MHz on a 1333MHz bus.  If I set my bus
to 1600MHz, which runs the CPU at 3800MHz, everything reports CPU speed
correctly.  However, if I run my bus speed anywhere in between 1333MHz
and 1600MHz, the CPU speed is *not* correctly reported.

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https://bugs.launchpad.net/bugs/379873

Title:
  CPU Frequency Scaling Monitor reports incorrect CPU speeds when
  overclocked

Status in linux package in Ubuntu:
  Expired

Bug description:
  The reported frequencies of an overclocked Core 2 Duo are incorrect.
  Benchmarking and performance testing can confirm that the CPU is
  running at the overclocked speeds, but the values reported through
  cpuinfo are the standard stock speeds.

  CPU has been overclocked from stock 3.00GHz to 3.60GHz. This can be
  confirmed through dmidecode (output attached). The issue is that
  cpuinfo (and related utilities) all report the stock CPU speeds
  instead. This is only a visual/reporting issue. The CPU is still
  throttling correctly, and the speed is correct as per the overclocking
  ratio.

  i.e. (tested and confirmed in benchmarks & Bogomips)
  Reported 2.00Ghz = (3.6/3.0 * 2.0) = 2.40GHz True Clock Speed
  Reported 3.00Ghz = (3.6/3.0 * 3.0) = 3.60GHz True Clock Speed

  There are a few reports of this in the Ubuntu forums, however no
  resolution had been found. I have updated the BIOS on my motherboard
  (ASUS P5Q) to the latest available, with no changes. All other BIOS
  options are per standard - allowing CPU throttling/etc.

  Bug #132403 makes reference to this similar issue, but this is not a
  BIOS problem, only a reporting problem.

  Compare:
  cat  /proc/cpuinfo
  cpufreq-info
  dmidecode --type processor

  Only dmidecode is reporting the correct CPU speed as set in the BIOS.

  Regards,
      Robert.
  --- 
  Architecture: amd64
  DistroRelease: Ubuntu 10.04
  InstallationMedia: Ubuntu 9.10 "Karmic Koala" - Release amd64 (20091027)
  NonfreeKernelModules: nvidia
  Package: cpufrequtils 006-2
  PackageArchitecture: amd64
  ProcEnviron:
   LANG=en_NZ.utf8
   SHELL=/bin/bash
  ProcVersionSignature: Ubuntu 2.6.32-24.38-generic 2.6.32.15+drm33.5
  Tags: lucid
  Uname: Linux 2.6.32-24-generic x86_64
  UserGroups: adm admin cdrom dialout lpadmin plugdev sambashare vboxusers

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