I loaded up both a 44.12 vanilla install and an old .30c install. In both, points were shared between skills and items.
I suspect I know what is causing the confusion, though. The way vanilla works is that the default embark loadout is set up so that there are normally 200 or so points spare after accounting for all items. That point pool is shared between both skills and embark items. The numbers to the right of the skills (that start at 5, and go 6, 7, 8, 9, 10 as you increase skill proficiency) are the costs that are taken out of that pool. In addition, each starting dwarf gets 10 skill points, and each skill increase costs 1 point. When increasing a skill, you must have a point available from the dwarf and the 5-9 points available from the shared pool. However, unless you are handing out more than about 5 skill points per dwarf, you will never hit the 200 shared pool limit before allocating all the points you want to allocate.
If you are not playing vanilla, then the changed prices from modded items may affect how many points you have spare after accounting for a standard loadout. You may have less, you may have more, in some extreme cases you may have no points left (and you can get free points selling back all the expensive modded items that inflated your point pool). In any case, your problem is probably that Masterwork's changed pricing is reducing the amount of points you have available after buying a default loadout. Of course, the solution is quite simple. Sell some of the default loadout to make room for skills. This shouldn't be hard since the default loadout has a lot of unnecessary metaphorical fat that can be cut.
