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What you're describing is the way it works. There isn't a way to include the "pre-sim" stats into the leaderboards. This is just how the program got developed. Originally, the career stats weren't even imported. The program was designed to work on the current stats in the game, the career stats don't have the detail needed for many of the calculations.
After many requests, I started importing the career data. But, I found importing the data was very unreliable-alot of data would not get imported. In fact, I only recently (version 5.3.2) made improvements to reading those files so that now (I think) most of the career data is getting imported. Since I couldn't reliably get the data and the data didn't contain the detail of the current stats, I just used it as an informational display on the player pages and not for anything else.
Even though the importing problem has been solved, the fact remains that some of the leaderboards still can't be done because the data is simply not there. I don't think I want to have some leaderboards use the pre-sim stats and some not.
As for why your career files are missing the 2000 season, I'm afraid I don't have any helpful advice on that one.
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