Caltrain introduced a $0.25 base increase on Jan 1, 2009. However, no schedule change took place in January. According to my sources at Caltrain, they simply misprinted the paper schedules with the notice. That explains why their website does not mention any schedule changes. The actual schedule change will take place in March 2009, and will be announced in Feb.
iCaltrain App v1.0 and the web app remain up-to-date on its schedule info. App v1.0.1 is now available in the App Store and shows the updated fare. I had hoped to get it into the App Store before the New Year, but I had to take several weeks off in December due to health reasons.
The March 2009 schedule change will be included in the free, v1.1 update, which I expect to submit to the App Store in mid-Feb. Schedule updates beyond 2009 will be released in a future version of iCaltrain.