1. Create a new plugin with and put the following line in version.php:
$plugin->cron = 0

2. Install the plugin to a Moodle server.
3. Update version.php, changing the $plugin->version number and setting the cron line to, for example:
$plugin->cron = 60

4. Visit the admin/notifications page to upgrade the module

Expected outcome:
'mdl_modules' database table now contains the updated 'cron' value for this plugin (i.e. it should be '60')

Actual outcome:
'mdl_modules' database table still has the original 'cron' value ('0')

Workaround:
For the moment, I've added a manual upgrade to the cron value in 'mypluginname/db/upgrade.php', but would prefer not to have to do that.