My car is weird like that. Sometimes it is notchy going from 2nd to first. But, all of the other gears are pretty smooth.
However mine is notchy when it is cold and/or while coming to a stop... so I have no idea what causes it. It's something that comes and goes so I don't worry too much about it. Maybe synchros going bad?
I just had the tranny fluid flushed and replaced a month ago, I have the stock clutch, and the car has 50k miles.
I think it's just the way our T-45's wear man... not much you can do. Unless like you said it is a clutch issue or something.