We've been quite open that we have no intention of a) knowing what you do, and b) punishing you
BUT if all of your traffic is via VPN and is picked up as irregular it may in fact flag it. I just don't know enough about your specific use-case to answer that, nor do I know the precise details of the algorithms to tell you exactly when you're going to be flagged.
It boils down to your experience. An ISP can build systems and processes to their heart's content with the best intentions, and someone is still adversely affected. No ISP will ever please absolutely everyone. The guy trying to download 2TB on a R200 account is in all likelihood going to complain that his internet experience is poor, while everyone else is perfectly happy. We can only do all we can to please as many people as possible. Our goals are to please the mybroadband community - in our opinion the most discerning internet user in SA - if we can do this, we can please just about everyone.
MyBroadband users in particular have incredibly high demands of an ISP given the current telecommunications environment, and many have done a good job in trying to accommodate this. Others have lied and connived their way into the market. We won't be the latter.