I think its more of the context that the two are used.
The term "I'm sure" is more weak, in a matter of speaking. Its like saying "I'm sure I left the car keys on the table, but I can't find them". It's as if you're justifying to yourself that to your knowledge this event / subject existed / happened. Although, using the term "I'm certain" in this situation would not be wrong. It would still make sense.
Personally though I think the term "I'm certain" has more weight behind it. Its more of a definite statement. "I'm certain of this....".
Overall, I'd say you can get away with using them interchangeably.