Why do some Mormons abstain from drinks with caffeine in them?

We need to be careful and check our facts before we go and label caffeine as "harmful." While it certainly CAN be, so can water - you can die from water intoxication. There are many positive effects of caffeine.

Caffeine is an ergogenic: increasing the capacity for mental or physical labor. A study conducted in 1979 showed a 7% increase in distance cycled over a period of two hours in subjects who consumed caffeine compared to control tests. Other studies attained much more dramatic results; one particular study of trained runners showed a 44% increase in "race-pace" endurance, as well as a 51% increase in cycling endurance, after a dosage of 9 milligrams of caffeine per kilogram of body weight. The extensive boost shown in the runners is not an isolated case; additional studies have reported similar effects. Another study found 5.5 milligrams of caffeine per kilogram of body mass resulted in subjects cycling 29% longer during high intensity circuits.

Caffeine citrate has proven to be of short and long term benefit in treating the breathing disorders of apnea of prematurity and bronchopulmonary displasia in premature infants. The only short term risk associated with caffeine citrate treatment is a temporary reduction in weight gain during the therapy, and longer term studies have shown lasting benefits of treatment of premature infants with caffeine.

Caffeine makes pain relievers 40% more effective in relieving headaches and helps the body absorb headache medications more quickly, bringing faster relief.
Several large studies have shown that caffeine intake is associated with a reduced risk of developing Parkinson's disease (PD) in men, but studies in women have been inconclusive.

According to one study, caffeine significantly reduces the risk of heart disease in epidemiological studies.
There is no scientific evidence for the mistaken but common belief that caffeine consumption causes stunted growth in children.

I'm sure the "higher-ups" know about those of us with a "problem" with caffeine, and I think it is safe to say that if caffeine truely was not allowed, they probably would have cleared up the confusion and said so by now.

P.S. There's a good talk by Elder Quintin L Cook, of the twelve, entitled "Looking Beyond the Mark." And I quote:

"Certain members have wanted to add substantially to various doctrines. An example might be when one advocates additions to the Word of Wisdom that are not authorized by the Brethren and proselytes others to adopt these interpretations. If we turn a health law or any other principle into a form of religious fanaticism, we are looking beyond the mark."

"When we look beyond the mark, we are looking beyond Christ, the only name under heaven whereby we might be saved. Elder Jeffrey R. Holland of the Quorum of the Twelve Apostles said, "Jacob saw that the Jews would look 'beyond the mark' and stumble in their search for the Holy One of Israel, this literal Son of God to be known as Jesus Christ: 'By the stumbling of the Jews they will reject the stone upon which they might build and have safe foundation.'"