I dug into this a little bit, and found the culprit to be a combination of element.blur(); and the .on() handler. See the following jsfiddle:
Similar to the original commenter's fiddle, on Chrome clicking on both input boxes, neither allow you to enter keys into them because they .blur(); on focus();. The console reads "test2" whenever you click the inputs (as expected). If you take out the .blur(); command, you can type in both inputs and "test1" is console.log'd on keyup, as expected.
In IE11, everything works the same way except when you have .blur() added in (like the fiddle starts with), you can still type in the input box ONLY on the input box whose event handlers were handled with a body.on() call, instead of assigning them directly (jquery.focus(fn)). Another note is that, as per the original ticket report, the keyup function does NOT get called when you input keys into the box.