You mean like that above ?
On 3 different attempts after quitting then re-booting I saved skills and must have used around 25 skill points, I even did the Dotposts without been detected and maxed out the left hand Skills but the right hand ones still would not unlock even when purchased.
In the end I started a new game but was gutted that I had to lose everything from my previous game - It seems that we can only have 1 saved game active at any time so I lost over 30 hours exploring
These skills have unlocked for others as some on my Friends List have the Trophy / Achievement so it could be isolated to small numbers.