The system.info file is simply the file containing information for the System module. As such, there should not be more than a system.info file in a Drupal site, except in the case you copied the Drupal core files more than once.
The system.info file doesn't contain any release value. It just contains a reference to a constant defined in another file.
name = System
description = Handles general site configuration for administrators.
package = Core
version = VERSION
core = 7.x
files[] = system.archiver.inc
files[] = system.mail.inc
files[] = system.queue.inc
files[] = system.tar.inc
files[] = system.updater.inc
files[] = system.test
required = TRUE
configure = admin/config/system
VERSION
is defined in the includes/bootstrap.inc file. If that file has been updated, it's probable the Drupal core release isn't reported correctly.