Why would you think it had anything to do with the save system? Nothing of the sort is mentioned.
It's due to a change in Chromium/Chrome v45 which intentionally breaks the HTML5 History API for files opened via the file:// scheme, as noted on these forums in this post from the SugarCube releases thread (among other posts about it).
A workaround is already in place. If you're using the version included with Twine 2, then you'll have to wait for the next Twine 2 release to get it. If you've installed a local copy of SugarCube, then just upgrade to the latest version.
When I switched story formats from sugarcube to sugarcane (to see if it was a problem was an error I made or something wrong with sugarcube), it said something about not being able to save the story. In any case, upgrading did solve the issue, thanks.
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It's due to a change in Chromium/Chrome v45 which intentionally breaks the HTML5 History API for files opened via the file:// scheme, as noted on these forums in this post from the SugarCube releases thread (among other posts about it).
A workaround is already in place. If you're using the version included with Twine 2, then you'll have to wait for the next Twine 2 release to get it. If you've installed a local copy of SugarCube, then just upgrade to the latest version.