The only thing I know for sure that Contador is doing at this race is making **** up every time he talks

I'm never one to believe the "I'm just here to train" line, especially from folks as hyper-competitive as those at the front of the peloton. I suspect Alberto covered for a bad time trial performance on an ill-fitting bike by making excuses about sitting up. Nothing new there - riders do it all the time. His attacks and his decision to follow Jani today didn't show a guy just getting miles.
On a somewhat-related note, are there time bonuses at stage finishes? if there is, it seems that he lost a few secs to Jani.