Thats weird… I use GSE3 PvE/PvP Macro 9.1 (No Fury Starvation And Never Gets Stuck) - Demon Hunter / Havoc - WoW Lazy Macros for my DH and if I move the macro button to lets say 1 and spam it, it works just as intended, only difference is, I cannot keep up with spamming the key over and over again at 50 ms 
So I think it is something on your end that is making it not do damage…
The dps loss with my mouse doing the clicking for me and me pressing the actually button is 3.4k dps vs 2.8… so yeah its a loss, but not one anyone would notice in LFR