I'm assuming nobody has explained skill queueing to you. With the way the GCD works, you can hit a skill up to around half a second before it's due and it will go off as soon as it can. It's a good way to make sure your ping to the server has no detrimental effect on your dps and most MMOs with a GCD use this. Of course if your ping is horrendous it might start to matter.

Anyway, this system does not apply to macros. Therefore every GCD skill you use when it's macroed will have your reaction time plus the ping to the server added to it. It's a pretty substantial loss in dps and something you should avoid as much as possible or altogether if possible. Things like mass macroing your buffs or having more than one off GCD ability tied to one macro are fine for the most part, but macros shouldn't include any GCD abilities.

Hope that helps with cutting down on your "problem".