Testing this with the current version of IE11 with all updates, the message box is shown twice and the HTTP form is POST'd to the server. As seen in Fiddler:
POST http://fiddle.jshell.net/echo/json/ HTTP/1.1
Accept: */*
Content-Type: application/x-www-form-urlencoded; charset=UTF-8
X-Requested-With: XMLHttpRequest
Referer: http://fiddle.jshell.net/CZGEH/6/show/
Accept-Language: en-US,en;q=0.5
Accept-Encoding: gzip, deflate
User-Agent: Mozilla/5.0 (Windows NT 6.3; WOW64; Trident/7.0; rv:11.0) like Gecko
Host: fiddle.jshell.net
Content-Length: 22
Connection: Keep-Alive
Pragma: no-cache
json=%7B%22a%22%3A1%7D
Please verify that you can reproduce this in No Add-ons mode in the browser, and verify that you do not have any 3rd party "Download Manager" plugins or other extensions (like Google Gears) that thunk IE's network stack installed.
Extensions using undocumented means to alter IE's network stack are known to have bugs which cause 0-byte POSTs.