I have a Drupal 7 multisite with CiviCRM multisite also and now on the new websites I have a twice the main menu bar :
I don't know how to fix this and haven't found a similar issue
Any idea ?
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Try enabling theme_debug with drush and check where this is coming from within the template system.
drush variable-set theme_debug 1
In chrome browser you can use the inspector to find the template suggestions and which template is being used printed as comments in the HTML.
Don't forget to turn off theme_debug when you are done
drush variable-set theme_debug 0