Thanks for answering my post.
I was able to solve the issue.
The code was actually running but I was unable to notice that because my only feedback was through the serial port which was at a wrong baudrate. (continue reading, its interesting)
That problem happened because while debugging I got exactly 9600bps with the configs I had. Therefore able to communicate with my desktop software and develop everything with no problems. After flashing the device the frequency moved to another range but I wasnt aware about that change.
The change happened because when you download the code for debug purposes the tool/codewarrior seems to automatically set a few registers (ICSSC, ICSTRM, ICSC1 and ICSC2) (not sure if they are all needed, still did not had time to go in details) probably in order to communicate at a more precise speed during the debug. I therefore was getting the 9600bps with that configuration done automatically by the tools. While powering the board standalone with no proper configs on (ICSSC, ICSTRM, ICSC1 and ICSC2) it was not communicating and my first thoughts were that the code was not running but it was but god know at what baudrate. (no scope/data acquisition tool here to measure).
After realizing this I got compared the configs (original versus the ones appearing during debug) and added to my code the ones I found during debug... and guess what? PROBLEM SOLVED.