I didn't know about those. Wiki says:
"In the mid- and late-90s, Kramnik, although considered one of the strongest players in the world, suffered several setbacks in his attempts to qualify for a World Championship match. In 1994, he lost a quarterfinal candidates match for the PCA championship to Gata Kamsky 1.5-4.5, and later that year, lost a semifinal candidates match for the FIDE championship to Boris Gelfand with the score 3.5-4.5. In 1998, Kramnik faced Alexei Shirov in a Candidates match for the right to play Garry Kasparov for the Classical World Chess Championship, and lost 3.5-5.5. In 1999, Kramnik participated in the FIDE knockout championship in Las Vegas, and lost in the quarterfinals to Michael Adams 2-4."
So it seems he has a pretty bad match record until the Kasparov match, but he was I think 2nd highest rated player (or maybe 3rd after Anand) when the organizers chose him as the challenger when Shirov and Anand refused the conditions, and was recognized as the possibly toughest challenger at that moment.
I don't think this bad match record before 2000 has much to do with the level of understanding of the game he reached. He is a class above Kamsky, Shirov and arguably Gelfand today.
Kramnik also lost a match to Kamsky at some point I believe and in his lost match with Shirov he couldnt win a single game. Did he also play a match with Gelfand ?