For myself it looks like the ini file is not used at all.
If there is an syntax error inside then it is ignored completely i think.
Here again my complete ini file and the agent output. It is really on the one option set here.
[global]
# Just output certain sections (e.g. for upper hosts)
sections = check_mk uptime df ps mem services winperf systemtime plugins local spool fileinfo
output
PS C:\Temp\cmk> .\check_mk_agent.exe test
<<<check_mk>>>
Version: 1.2.6p17
BuildDate: Sep 3 2015
Architecture: 32bit
AgentOS: windows
.....
34 0 large_rawcount
1086 0 large_rawcount
1088 1 large_rawcount
1090 0 bulk_count
1092 0 bulk_count
1094 5612 large_rawcount
<<<>>>
<<<>>>
<<<local>>>
<<<systemtime>>>
1660243654
You see no logwatch section.
If you can show your complete ini file i can check what it does on my system.