Hi Dave,
a few ideas (which you might already tried, not sure), so just providing some ideas:
- does it happen for a fresh workspace for that project too? Could be that there is a lot of history information in that workspace, so a fresh one might help
- I have found https://bugs.eclipse.org/bugs/show_bug.cgi?id=387202 (rather old) which could be related: could you try to empty your recycle bin to see if this has an impact? On Windows clean as well your c:\users\<user>\AppData\LocalTemp folder
- does it happen if you do a clean first too? Or if you delete the output folder (debug?) first? I'm wondering if this is an issue with the autobuild getting stuck with the amount of your files and directories somehow.
- does the console view give any information where it is stuck: the screenshot shows a (linker) map file, so I'm wondering if this is at the end of the build?
- are you using internal or external builder? Switching might change things?

I hope this helps,
Erich