CheckMK version 2.0.0P1 vs CheckMK version 2.0.0p16 (CRE): Agent takes nearly double time to answer

First things i see is a broken WMI on the monitored server.

Second point is - your disabled section looks like it is not recognized. Do you have somewhere an explicit enabled section defined?
I have only a “sections” point defined like this

global:
  sections: 
    - check_mk 
    - spool 
    - plugins
    - local
    - winperf 
    - uptime 
    - systemtime 
    - df 
    - mem 
    - services 
    - dotnet_clrmemory
    - wmi_webservices
    - wmi_cpuload
    - ps 
    - fileinfo 
    - logwatch 

and this results in the following output of the “showconfig”.

  sections:
    - check_mk
    - spool
    - plugins
    - local
    - winperf
    - uptime
    - systemtime
    - df
    - mem
    - services
    - dotnet_clrmemory
    - wmi_webservices
    - wmi_cpuload
    - ps
    - fileinfo
    - logwatch

exactly the same.

With the last lines you see that it only takes so long as it tries to get many WMI things that your system cannot provide.