It seems the modifications in the new shiparch are taken as cheating. Get the shiparch.ini from uninstall folder in the rar and use it. Tested and working. Will contact Alley to ask her for more info.
The new ini files for these ships were not originally added in disco and its protection is detecting them. With the "old" shiparch all is working fine because I've modified the path to the new cockpits without adding new ones. Sadly the ships below will not have "new" cockpits for now:
council gb/cr/bs (they will see "GRN" colors)
liberty battle transport
liberty train
liberty carrier
rheinland battle transport
slave liner
luxury liner
bretonia carrier