to OP: i know what you mean
It doesn't have anything to do with the sp/xp fatique and those 8+7hours of lvling. It's more like the rmt countermeasure that's also in ff11 where you have to change zones every hour or your results will go downhill.
In ff14 it seems to be worse though, as even changing the region didn't reset it for me :/ Most of the time i get this gathering-fatique after 2-3 hours of logging, then the success rating will quickly go to hell, even if a chop would have given me that item 100% it will just crit-fail 90% of the time. I'll then be happy to get even one item from 5-6 gathering attempts. Changing regions, repairing all my equip, even crafting for an hour and changing back didn't reset this status for me.
Only advice i can give is to just stop logging/harvesting for that day :/ change to mining/fishing/crafting or fight-classes and get back to tree-chopping the next day.
to Blazza
Yeah SE was just lazy with the node-placing <.> though i found some harvesting spots in strange places far far away from any choppable trees.