Rafael,
I am having this same problem where the Seeger JLink is not listed in the target configuration drop down. I was using v5.3 with the JLink without a problem. I upgraded to CCS v5.5 and now there is no support for JLink. listed in the drop down. I reinstalled the JLink drivers but no change. I reinstalled CCS, no change.
I am working with a Stellaris part LM3S6911. I am trying to make improvements to an existing system.
Also your response did not answer the original question posed by a bugsworstnightmare. Although the answer is verified it is not clear that the problem was ever fixed or what was done to fix the problem. The only thing that is clear is that you have JLink is working on your system. How you made that work is the information needed.
This seems to be a typical situation with CCS. When ever I change some thing with the CCS environment it seems to start a new series of unrelated problems.