Hook into Panels content form submit
Correct, according to the panels.api.php file, hook_panels_pane_update() is for changed panes.  There's one just above it for new panes called hook_panels_pane_insert().

If you want the same function to happen every time regardless of whether the pane is new or not, combine them like this:

function mymodule_panels_pane_insert($pane){
  mymodule_act_on_panels($pane);
}

function mymodule_panels_pane_update($pane){
  mymodule_act_on_panels($pane);
}

function mymodule_act_on_panels($pane){
  //Do the things here
}