I have no problem on two Macs running Mac OS X 10.9.2 with InDesign CC 9.2.
Have you started by restoring your preferences. Here's how:
If you use the delete folder method, remember that in OS X 10.9, the <Home> library his hidden. In the Finder, hold down the Option key, and choose Go > Library to make it visible.
Thanks for the reply, I tried dumping the preference but still no joy. Could I ask what platform your server is running on?
The reason I ask is because initially I thought the problem was between OS X 10.9 and our Xinet mounted volume(s), I logged a call and was told by Xinet this is a wider spread issue and the problem is happening to other AFP mounted volumes not just Xinet.
Sorry, I didn't read your posting closely enough.
I have no server and have no way of testing with a server. My apologies.