Update:
Took the car to the local p-car shop and there were no fault codes for the transmission. He said the next step is a transmission service (fluid/filter change). If that doesn't work, I guess its supposedly something internal in the transmission and i'd have to get a new one. ...or in my case, scratch the car
I just can't understand (and I don't know much about transmissions) how it would be an internal problem if it shifts fine in manual mode though. Any thoughts?