CHECK_METHOD = modtime is not working as expected due to a regression in 9.x as there is wrong calculation which will lead to un-expected re-reading of a file.
Until next patch, use following workaround for inputs with CHECK_METHOD = modtime
In inputs.conf set following for impacted stanza
time_before_close=0
I'm seeing this issue on 9.3.0. Which version of 9.x.x was this patched?
9.2.1 and above has the fix. May be you want to explain your issue with configs.