Well, something like that seemed to be the problem. I cannot tell you which were the conflicting files because I removed all the extensions prior to your reply. Although I updated everithing using the update tool from the S32DS.
Solution was removing all extensions and updates and installing the SW package from the "RD-HVBMSCT800BUN reference design bundle" so probably I was missing something?
That did the trick for since I only need to see the pins with the configuration tool.