I do not have access to a computer with Windows installed. Could you give me some Javascript errors or some hints what could be wrong?

From the jsPlumb documentation, this is the only comment regarding problems with IE:
"jQuery 1.6.x and 1.7.x have a bug in their SVG implementation for IE9 that causes hover events to not get fired."

So it should work in theory. Is this a css problem?

I don't have access to a win PC @home either, therefore I followed this instructions to get a VM up and running on my MAC: http://osxdaily.com/2011/09/04/internet-explorer-for-mac-ie7-ie8-ie-9-free/

After this, you can run your normal test-env with a specifig port (sudo mvn hpi:run -Djetty.port=80) and from within IE in your VM you can access it with this address: http://10.0.2.2 . Don't forget to change the "Jenkins URL" in the gloabl config to "http://10.0.2.2" too, otherwise you CSS will not load (that was my first error)

By going through my setup I found that I forgot to change "Jenkins URL" and after adjusting it, I got a bit further, the boxes are now displayed, but they look really ugly (see new screenshots).

The only warning I get in IE is this one: "SEC7115: :visited and :link styles can only differ by color. Some styles where not applied to :visited. jsplumb"

While reading through the jsplumb documentation, I found this:

...if, for some reason, you set the render mode to be jsPlumb.VML but you're in any browser other than IE, jsPlumb will use SVG.

so I changed...

from: jsPlumb.setRenderMode(jsPlumb.SVG);
to: jsPlumb.setRenderMode(jsPlumb.VML);

it might be OK, but it did not really change anything.

Unfortunately I'm away for about the next three months so I'm not able to work on this...