I am importing a batch of products via Commerce feeds and I have to manually edit the node and enable auto aliases.
I have the Pathauto module enabled.
Why is it disabled?
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Run the status report and see if there are any problems with the Pathauto installation. Also check the Drupal logs.
If no problems are seen, check the Pathauto preferences and see if something disables its functionality there.
Also make sure no one changed the core files of the module and if you're not sure, just reinstall and repeat the process.
Note_1: You could always bulk-create auto aliases for all your non-aliased nodes and this bulk action will automatically create aliases that will appear on screen, instead of the permalinks (node/#). In any case, this should be done automatically.
Note_2: Make sure to flush all caches when you are done, and after that, flush the browsers cache (trust, me it could help in this specific case).