Sorry, I missed this thread somehow...
Can you submit a bug report so I can get more info (pm version, unity version etc.). If you can attach a small repro project to the bug that would be great! But I'll try to repro here either way and let you know what I find...
EDIT: I did a quick test making an FSM that sets global variables, disabling and enabling the GameObject and globals were still updated. So I need more details to reproduce the problem you're seeing... first step is the bug report since that will give us more info on your setup.