I have CCSv5.5 running in Ubuntu 13.10 also. Everything is working fine. i was able to update to C2000 compiler version 6.2.5.
Not sure what is going on with your install. It looks corrupted somehow. You can try a new install or if you don't want to bother, you can simply manually download and install it.
http://processors.wiki.ti.com/index.php/Compiler_Installation_and_Selection
Thanks
ki