Still skipping nodes. Just watched it skip 3 within close proximity (could see them on the mini-map). 
They weren't underwater or by elites. Using Drogo's profile. 
Not sure whether it's a bot issuse or profile issue but thought i'd report it anyway 

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Def not profile issue, My suggestion is
Delete hb cache
Set wow to auto loot
restart wow, hb
see how it goes then.
But yes, gb2 has been skipping nodes in dread wastes since Mop was released, there are many threads on the subject.
I would recommend only farming dread wastes if u specifically want fools cap and even then run it overnight since it needs a good 5-7 hours to get any good results.
last run thru dread wastes using my public profile
[Gatherbuddy2]: Stopped gatherbuddy after gathering 214 nodes in 4h 8m 14s.
[Gatherbuddy2]: Fool's Cap: 78
[Gatherbuddy2]: Ghost Iron Deposit: 71
[Gatherbuddy2]: Green Tea Leaf: 49
[Gatherbuddy2]: Rich Trillium Vein: 1
[Gatherbuddy2]: Rich Ghost Iron Deposit: 8
[Gatherbuddy2]: Sha-Touched Herb: 4
[Gatherbuddy2]: Rich Kyparite Deposit: 1
[Gatherbuddy2]: Trillium Vein: 2
1 node per 2min average
Hope my suggestions help