I recently watched Donnie Darko again on Blu-Ray, which reminded me that I love that movie. But I was always confused as to what truly happened during the movie. Did Donnie ever have a conversation with Roberta Sparrow, or was the letter his only communication? Did Frank go back in time to make the world better for Donnie before he died? Did Donnie travel back in his mind to create better images in his memory before he passed on? What is the day that Donnie has his first, non-fatal run-in with a jet engine? Is Frank a representation of his own regret? Can he see the future because he's looking through the past? Was the school flooding/vandalism ordered so they would send in Jim Cunningham, who in turn would be revealed to have a secret obsession with child pornography? If the world reset, then does that mean every one of his actions had no bearing when everything was wiped? Did Donnie know he was going to die when he saw the wormhole over his house, and if so, did he know he had to do it to save the world? Did his comment about being a superhero reveal how he felt when he was going back and making the world a better place? Since he mentioned that he could build a working time machine, does that mean he did and was using it?
I am so confused, yet I love all the ideas that float into your head when you watch this movie.

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Can't help you out cause I haven't seen it in 5 years, sorry :(
You should check out Southland Tales though, I loved that movie.

I'll have to watch it again, before being able to comment on anything. But have you seen this:
http://www.donniedarkofilm.com/
It may or may not answer your questions/confuse you more. You might also want to see if Wikipedia has anything on the film (and more importantly, useful links to better information).
I also want to see the semi-sequel, but no idea if it's ever seen release or will ever see an international release.

Oh, the sequel S. Darko was released, and it was shit. It was made by different people, and they just threw themselves into creating uninteresting characters and referencing the first movie whenever possible.

I haven't watched it in a long time but i think the flood and fire where part of the elements he needed to go back in time or something that's why he did them.

i saw the box last night by the same director was interesting and mysterious with a few interesting twists

Watched this movie quite awhile ago.
The story was very confusing, had to read the whole story from wikipedia and IMDB to understand what was going on.
For what I can remembered, it was pretty decent.

I enjoyed both renditions (orignal and directors cut) and it is very well acted. Its so much leaner and interesting than the bloated "southland tales" I think it is better not to have explanations and just ponder them in this case - I remember listening to a commentary on the director's cut and he brought up aliens in a description of one of the changes between the versions. I am not convinced that thought was helpful in my enjoyment of the films.
[edit - back to the original topic] I haven't seen either movie in a few years and I cannot remember enough details to be very enlightning - but some of those thoughts are quite interesting and will have to keep in mind next time I watch it.