For want of a better name, this seems to happen in Webkit browsers after leaving the Twine game alone for 5-10 minutes. When you come back, it seems to take a couple of seconds to start up again, so you hover your mouse over a link and it doesn't light up for a couple seconds. Once it's done its "reloading" it's snappy from then on.
Firefox doesn't seem to have the issue.
Is this just a Twine thing, or potentially something I'm causing through heavy asset use and story size?