Hi,
A few details caught my attention: what version of CCS are you using? Also, you mentioned Segger's command utility, but I just wanted to double-check: did you install the Segger device drivers from their downloads page?
The Jlink for CCS only supports up to CCSv5.5 at this time, and it only provides the emulator driver to interact with CCS - you still need to install Segger's device drivers for Linux to properly initialize it.
I don't have the same board as you, but I have a BeagleBone white with a cTI 20-pin connector and I connected my Jlink Base emulator without problems.
I am using VMware Workstation 10 with Ubuntu 12.04/64 and CCSv5.5 and Segger driver version 4.86.1. Both CCS and the driver were installed with superuser privileges.
Also, it seems the utility JlinkExe does not work properly (or I just don't know how to use it). I get the same output as you, either running as a regular user or as superuser.
Apart from this unfortunately I am not sure what else to try, but I will reply if I have some additional ideas, ok?
Regards,
Rafael