Very important, that the weight of this module in the system table will be larger, that the Pathauto. (Defaults: Inherit - 0, Pathauto - 1)

In this, default case, when somebody edit a saved node, that have inherited fileds, pathauto will see the wrong (the parent) content type, as $node->type in the hook_form_alter. At the second call it is ok, but pathauto already set its variables, and not set again. Conclusion: If the patterns (the generated path alias) are different for this types, then pathauto will turning off the automatic alias generation.

Solution: Change the weight of the Inheritance in the system table to larger, than pathauto. (E.g. 2)