Eclipse + Openfire 3.9 onwards not importing correctly

Have some time this weekend to spend on Openfire duties but struggling to get Eclipse to see the new 'Openfire' git repo I've just checked out.

Following the instructions below as I've done dozens of times before but Eclipse completely scrambles the repo src paths. No issues checking out the SVN path. Any suggestions?

http://community.igniterealtime.org/docs/DOC-1020

Just to add it affects Git and SVN trunk (3.9). Checking out 3.8.2 SVN tag imports just fine.

Here's the 3.8.2 project, Eclipse imported it perfectly:

Here's the 3.9.X project, Eclipse screwed it up:

Repeated this process about 3-4 times now and it has the same result everytime.