Here is my proposal for the issue described, though I haven't been able to reproduce the issue on a clean nor upgraded site. Would appreciate feedback.

in admin/includes/init_includes/init_user_tracking.php

Locate this portion of the code:
Code:
$installers = scandir($module_installer_directory, 1);

$file_extension = substr($PHP_SELF, strrpos($PHP_SELF, '.'));

while (substr($installers[0], strrpos($installers[0], '.')) != $file_extension || preg_match('~^[^\._].*\.php$~i', $installers[0]) <= 0 || $installers[0] == 'empty.txt') {
  unset($installers[0]);
  if (sizeof($installers) == 0) {
    break;
  }
  $installers = array_values($installers);
}


if (sizeof($installers) > 0) {
    $newest_version = $installers[0];
    $newest_version = substr($newest_version, 0, -4);

    sort($installers);
    if (version_compare($newest_version, $current_version) > 0) {
        foreach ($installers as $installer) {
            if (substr($installer, strrpos($installer, '.')) == $file_extension && (preg_match('~^[^\._].*\.php$~i', $installer) > 0 || $installer != 'empty.txt')) {
                if (version_compare($newest_version, substr($installer, 0, -4)) >= 0 && version_compare($current_version, substr($installer, 0, -4)) < 0) {
                    include($module_installer_directory . '/' . $installer);
                    $current_version = str_replace("_", ".", substr($installer, 0, -4));
                    $db->Execute("UPDATE " . TABLE_CONFIGURATION . " SET configuration_value = '" . $current_version . "', set_function = 'zen_cfg_select_option(array(\'" . $current_version . "\'),' WHERE configuration_key = 'CONFIG_" . $module_constant . "_VERSION' LIMIT 1;");
                    $messageStack->add("Installed " . $module_name . " v" . $current_version, 'success');
                }
            }
        }
    }
}
And modify/replace to like the below (with code that causes a difference highlighted in red):

Code:
// Obtain a list of files in the installer directory.
if (is_dir($module_installer_directory)) {
  $installers = scandir($module_installer_directory, 1);
  // Determine the extension of this file to be used for comparison on the others.
  $file_extension = substr($PHP_SELF, strrpos($PHP_SELF, '.'));
  $file_extension_len = strlen($file_extension);
  // sequence the installer files to support stepping through them.
  if (sizeof($installers) > 0) {
    sort($installers);
  }
  // Step through each installer file to establish the first file that matches the search criteria.
  $newest_version = $installers[0];
  $newest_version = substr($newest_version, 0, -1 * $file_extension_len);
  while (substr($installers[0], strrpos($installers[0], '.')) != $file_extension || preg_match('~^[^\._].*\.php$~i', $installers[0]) <= 0 || $installers[0] == 'empty.txt' || version_compare($newest_version, $current_version) <= 0) {
    unset($installers[0]);
    if (sizeof($installers) == 0) {
      break;
    }
    $installers = array_values($installers);
    $newest_version = $installers[0];
    $newest_version = substr($newest_version, 0, -1 * $file_extension_len);
  }
  // If there are still installer files to process, then do so.
  if (sizeof($installers) > 0) {
      $newest_version = $installers[0];
      $newest_version = substr($newest_version, 0, -1 * $file_extension_len);
      if (version_compare($newest_version, $current_version) > 0) {
          foreach ($installers as $installer) {
              if (substr($installer, strrpos($installer, '.')) == $file_extension && (preg_match('~^[^\._].*\.php$~i', $installer) > 0 || $installer != 'empty.txt')) {
                  if (version_compare($newest_version, substr($installer, 0, -1 * $file_extension_len)) >= 0 && version_compare($current_version, substr($installer, 0, -1 * $file_extension_len)) < 0) {
                      include($module_installer_directory . '/' . $installer);
                      $current_version = str_replace("_", ".", substr($installer, 0, -1 * $file_extension_len));
                      $db->Execute("UPDATE " . TABLE_CONFIGURATION . " SET configuration_value = '" . $current_version . "', set_function = 'zen_cfg_select_option(array(\'" . $current_version . "\'),' WHERE configuration_key = '" . $module_constant . "_VERSION' LIMIT 1;");
                      $messageStack->add("Installed " . $module_name . " v" . $current_version, 'success');
                  }
              }
          }
      }
  }
}