bone armor does not get synergies by +skill wall & prison.
only hard points count.
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I cannot replicate this. I pulled up my P/B necro (Hell game difficulty) and removed all +skill gear from him, then checked the tree.
Bone Armor 1
Bone Wall 1
Bone Prison 19
With that point allocation, Bone Armor absorbs 320 damage with a single, un-boosted skill point. If the synergies were not being applied, it would only absorb 20 HP worth of damage.
My guess is you had a bugged game load resulting from one of those FUN crash-to-desktop events having corrupted something. Hit the gear icon next to the “Play” button in the BNet launcher, and select “Scan and Repair.”
You are correct, + to skills from items does not apply synergies. For anything. The + to skill just helps the base skill.
…or perhaps I misintepreted what I read. Never mind. 
I’m pretty sure no skills get +points to synergies. Blessed hammer, for example, or BO…