If it's not 'sorted out' in Linux, it's not 'sorted out' in Windows. :\ It's same code either way, just that command line is something Linux users don't object to very often. Now I don't admin any server that runs Windows (ok, call me a linux bigot ... I confess!). But, how about the direct link shown on the 'work-around-links' @ http://sos.tcea.org/tsmoodle.html
To my way of thinking, even Windows server administrators should appreciate the scripts in admin/cli/ cause using them in combination with git, the scripts can be included in a powershell script (couldn't they?) to run cron, backup the site code, do a mysql dump of the DB, put site in maintenance mode, pull new code via git, upgrade, and then take site out of maintenance mode. One can literally update the moodle in a matter of minutes and browser/web services issues are taken out of the loop.
However, if one just has to stay in the GUI and browser, Moodle still allows two browser instances from the same user, right? So .... launch one browser instance and take that instance to the page for enabling maintenance. When saved the page stays there. Don't click on anything. Open another browser instance to do the GUI upgrade - http://site/admin/. Heck, use Chrome or Firefox for that one cause there's no shared cookies/browser cache. When completed, come back to the browser instance that has the maintenance form displayed where one can set it to disabled and save again.
Still have two fall backs ... editing of config.php file which doesn't require reboot or restart of anything ... just access via browser to Moodle login. And, my last choice ... mysql editing of mdl_config table for the variable to disable maintenance.
Funny isn't it ... you see all the time in these forums folks recommending keeping Moodle up to date, but it isn't really easy for Admin users to do that .... hmmmmmmm - a little dis-connect there me thinks. One of these days, Moodle will get to the level of WordPress/Joomla 2 or 3)/Webmin where updates/upgrades are built in to the admin interface.
We need some Windows scripting ace to put together and share a powershell script, huh?
'spirit of sharing', Ken