Hi @SumoSniper ,
I'm facing similar issues, but with a more complex macro structure with submacros modifying and checking global variables. I haven't investigated too deeply but have been able to get around all issues so far by adding some M598's. First randomly at the start of every macro that is being called and at various points inside the macros. I settled on placing M598's after calls to macros that could modify a global variable that i will need later on and before i check/use a global variable that could have been modified by a macro.
Due to time constraints i could not investigate too far or boil it down to test cases, but i figured it's because of the deferred queue. Now macros called from jobs behave just as theones being called when no job is running.
I hope to have some time to read up more on this topic at some point. It would also help if the documentation had some examples of what could go wrong for people using only 1 motion system but trip over some problems with macros, meta commands and queueing etc.
Hope my "advice" could help out 
Cheers