I did a quick search and didn't see anything along these lines mentioned before, and know it has been an issue for people in my guild in game.
For those fights where you have to full burn a secondary target as soon as it pops, people typically make one or two /target macros. But if you spam your macro before the secondary target is there you usually end up targetting some random person that isn't who you're supposed to be attacking.
So I tried doing this last night and it seemed to work like a charm. You may want to through a /startattack at the end of it if you're melee though just in case.
/target Secondary Target
/target [help] Primary Target
So for example:
/target Demon Chain
/target [help] Terestian
/target Spitfire
/target [help] Fathom