You're saying the save action sometimes changes the value of a global variable? The thing is logically that's not possible since the save action shouldn't modify anything, and if it did it should be reliably happening. But that's just based on my experience.
Let's take a step back though. The two possibilities is the issue is either with C2 or with your events.
You can absolutely check if C2 is to blame by setting some text with that variable right after like this:
set text to globalvar
save
set text to self.text&" "&globalvar
If the two values ever differ then C2 is to blame and I'd hope a bug report could be made so Scirra could fix it.
If they're always the same then the issue is elsewhere in your logic. This would be a case where it would be nice if the debugger let you step through events more. Regardless you can also do text debugging like above, the browser log action is also useful instead of just text objects. Basically find all the places that set that variable in the event sheet and log it. Then when you run your game and you see the variable change you can pause and look in the log. You can even save the event number in the log text like so to know what event is changing it.
browser log "event 10: set global to "&globalvar
Anyways that's just some ideas into hunting down the cause.