iMac 5K Occasionally not shutting down!

Hi I have an iMac 5K i7 4GHz with 256 Internal SSD & 32 GB Ram.

With it I use the LaCie Little Big Disk 1TB Thunderbolt 2 SSD.

I have this unusual problem that occasionally the iMac does not shut down when either using key commands, or from the finder menu.

The dock and top menu bar disappear but thats it. I'm left with just my desktop picture and no shut down.

If I go to the dock with my mouse it pops back, and if I open up an application...iTunes for example the top menu bar reappears.

I have to use the on/off button at the back of mac. Its annoying as ****. This can happen with iMac being switched on for a little or long while. There is no excessive fan noise or heat related problems. I have done a hardware test, again no problems reported.

It's as though something is still working in the background, not allowing it to shut down.

I have ejected the LaCie drive before shutdown but still no use. I have also reinstalled Yosemite and reset PRAM etc.

Any useful suggestions would be most welcome.

Has anyone else experienced this with any of their macs??