I have found in some odd cases that if you log in while in combat macros will not work. Example: I had issues with something while in a raid and re-logged while I was re-logging someone pulled the boss putting the raid in combat. Upon loading in I was able to use GSE macro. I have experience this is in different occasions sometimes if i log out in a zone and when logging in there is a mob super close that puts me in combat and unable to use macros. Is there any fix for this?

Yes - don’t login in combat.

GSE doesn’t directly execute your macro. It programs an object which you “click”. Once combat starts GSE cannot make new objects nor can it change an existing object. It has to wait for you to get out of combat before it can finish initialising. This is a limit imposed by WoW’s combat sandbox. Once you are out of combat though it will finish setting things up.