This is a minor annoyance of TripIt but one that I put up with for the sake of the other features/benefits it offers. If is really just reading the times from the reservations emails so if you specify the 5pm arrival time in the hotel reservation and the 3pm car pick-up (and if the confirmation email also includes that) then they should show up in the correct sequence.

Kayak Trips does an auto-detect thing where they try to figure it out but I've had just as many problems with that as I have with the TripIt setup. Plus Kayak doesn't have a dedicated app for Trips so using it on the road is rather annoying.