Over the last few weeks I have started to use spotlight more and more. This is mainly as I am now almost entirely on my Mac. I started to notice a few issues with my top menu bar and decided to have a look at what could be causing it. It is quite odd that launching Eclipse from Spotlight is the cause. SystemUIServer becomes unresponsive.
Looking into it a bit more it appears as the only way to fix this is to just not launch eclipse from Spotlight. Oh well!