sogo.conf sets a default value for new users. If a user has already saved her preferences, the settings will no longer be affected by the defaults values found in sogo.conf.

Also check SOGoRefreshViewIntervals settings in sogo.conf

ok for the default value for new users.
But I don't understand why the graphical interface of a old user doesn't propose to change the refresh view.
There is only the "manually" option available and not the others.
We should see the different options on graphical interface : every_minute, every_2_minutes, every_5_minutes ,every_10_minutes, every_20_minutes, every_30_minutes, once_per_hour
no ?

What have you set for SOGoRefreshViewIntervals in sogo.conf?
What has the user set for SOGoRefreshViewIntervals?
sogo-tool user-preferences get defaults ${USER} SOGoRefreshViewIntervals

In sogo.conf :
SOGoRefreshViewCheck = every_minute;
SOGoRefreshViewIntervals = 1;

For user :
SOGoRefreshViewIntervals: "1"

That is your problem.
SOGoRefreshViewIntervals is an array Therefore:
SOGoRefreshViewIntervals = ( 1 );

Thank you very much. That's exactly what it is.
Sorry for the inconvenience. I'll read the documentation again :)