I've finally got my Windows 8.1 PC back up and running, and have been testing out Cryptograms.org on IE11 for quite some time now without a crash - is there a particular page that this seems to happen on? Is it the game page, or the game over page, or... ?
Reading up more on the issue it appears that at least some users who are experiencing periodic IE11 crashes immediately after upgrading to Windows 8.1 are finding that the issue goes away when they update the drivers for their video cards. More information on that is available here:
... though honestly, its probably just easier to switch to a better browser. Internet Explorer is no notoriously slow, buggy, and open to various forms of cyber attack, that its no surprise Chrome and Firefox are eating up more and more of their marketshare every month.