I'm having the same problem on my 96 Caldina. If I don't fully depress the clutch pedal when changing from 2nd to 3rd, there's a nasty noise as my gearbox teeth try to leave their natural environment.
I have changed the clutch to a Celica uprated one, so maybe the clutch spring isn't exactly the same.
Is it possible to put a new longer slave piston or similar to get rid of this problem?