Strange. I searched the web, and one person reported this in Tutorial: USB CDC with the KL25Z Freedom Board | MCU on Eclipse back in 2013, but no indication of a solution.
Can you share what you are using as host machine (Win7 64bit?).
Can you try to launch Eclipse as administrator, maybe this helps?
Are you using a special license file (C:\Freescale\CW MCU v10.6\MCU\license.dat)? Can you rename that file (so Eclipse does not find it) and retry if this changes anything?
Can you disable temporarily any firewall/virus scanner? It could be that it blocks access to some files? Are there any files put/blocked by your virus scanner?
I'm just digging what it could cause something like this.