Hence this didn't work for me, I came up with my own solution: tweaks.klickagent.ch/#30.05.2014_TwitterBootstrapCenterModal (just in case for someone this does not work either)
This is just matter of applying some CSS to the pleaseWaitDialog ID. You have to set position:absolute and the margin-top and margin-left need to be half of the height and width. So your CSS should look something like this:
This works. For anyone else with the same issue, I removed the height and position attributes and changed margin-top to -90px.
You will need to play with the numbers in order to achieve the box size that fits what you want but that should get you started.