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After enabling pathauto on an advanced project, I realised that the usual checkbox in the "path" tab was missing and that aliases were not generated.
Digging a lot, I found that core function
path_form_node_form_alter was called after
pathauto_field_attach_form what caused the
if (!isset($form['path'])) condition to fail.
I have been using pathauto for a lot of projects without any problem but I cannot figure why this is hapenning. I looked at the modules' weights in the system table and I found the issue here.
For an unknown reason, all my core modules had been weighted to 15 so they were called before and causing the issue.
Here is a patch to avoid this.