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It looks like hook_node_export_after_import_alter() is not being called in certain situations. The code starting around line 570 of node_export.module loops through the nodes to be imported, and (based on whether the node exists or not) sets the $save variable. Then, it saves the node if $save == TRUE. Outside of the loop, it checks $save and, if it's TRUE, calls drupal_alter('node_export_after_import') and shows the "!count of !total nodes were imported..." message.
The problem is that it's depending on the *last* value of $save. So, if the last node it tried to import was skipped, $save will be FALSE and the hook won't get called.
It seems like the hook should get called if *any* nodes are saved. Is this correct? Or am I missing something?
I'll upload a patch that fixed this for me.