AI Export Macro produces different output then manual AI export

I am trying to automate the export of an open file to Illustrator CS 6 format. I have found that the output is very different from when the same process is run manually. I have to assume there's some kind of issue with the macro, but what could it be? 

2K words worth of examples:

File exported while macro was being recorded:

Manually exported example

File exported by running the recorded macro:

Macro exported example

The macro is obviously killing all the transparencies but since it was recording my actions, shouldn't the macro produce the same results as the actions it was supposed to be recording?

Any suggestions on how I could make this work would be greatly appreciated.