On certain server setups, when installing or updating a module the Update Manager code will force the associated batch to be processed immediately from within a form submit handler. This means that any submit handlers that run afterwards will never run, since processing a batch calls drupal_goto().
The standard way to handle this situation is to let the form API initiate the batch process for you, since it automatically makes sure to process the batch only after all submit handlers have run. There's never really a good reason to call batch_process() yourself from within a form submit handler.
The attached patch makes the Update Manager use that method.