CPU clock slower after each resume from sleep

The issue you are experiencing has been reported many times.
Please refer to this bugzilla bug report.

The issue has been isolated to a particular commit in the kernel tree. That commit has also been backported to some previous stable kernel versions.
However, the actual real root cause is a Lenovo BIOS problem. Quoting from the linux-pm e-mail thread:

BIOS reports bogus passive trip point value, which is 0 degree Celsius ... In order to workaround this bogus BIOS, we should disable those invalid trip points by checking the trip point value,

If you go back a version of or two, your Lenovo will work properly (4.2.0-19 is known to work properly).

Your issue is not clock modulation (register 0x19A) related, unless your battery is below 30% (unproven, but suspected).

References:
http://ubuntuforums.org/showthread.php?t=2316101
Strange cpufreq scaling issues: regardless of governor, max cpufreq drops incrementally on wake
i3 throttled at 500Mhz when battery under 30%
http://marc.info/?t=145816738700001&r=1&w=2