I agree that I would err on the side of caution and assume that the one that shows higher usage is correct. The nice thing about prepaid though, is that either way, you won't get any nasty surprises due to overage.
I've noticed this glitch as well. After applying a data booster the other night, within five minutes, I receive a text stating that I've use 50% of my data. Check self-serve and I'm nowhere near 50%. Checked it again a few hours later, values are still the same, with usage well below 50%. I've really only seen this issue on two other occasions, but due to the fact that these occurrences were so far apart from each other, I figured it to be more a sporadic system glitch with no real cause for alarm.