I had the same problem with 2nd gear around 2k-5k miles. Now I have about 10k miles and its 3rd gear that does it. Also, after driving for a long time the clutch starts making soooo much noise it sounds like its gonna fly out of the car. When I push the clutch pedal in the sound goes away and comes back when I release it.(this has happened from day one)I took it in and they said, "nothing is wrong." Of course!
Gonna take it to another dealer soon see if I have better luck.

2003 track

 

mine happens too only when its cold but i thought this was normalcause once the car warms up it shifts just fine.

 

Dang +1 but on the auto transmission.

The first shift from first to second in the morning I feel a grind in the gears.

 

I had the same thing... took it to the dealer.. and now I am getting a new transmission.

It did that same "clunk" when going into 2nd.

 

I also have that cluck and i have to hold the clutch alittle longer after shifting to second otherwise the car bucks. anyone else have this, and what does it relate to.

 

i am actuly running into a problem shifting from second to third. At first i thought it was because I didnt; hav ethe clutch pushde all the way in, So i moved my seat forward so everytime i was touching the floor when i had the clutch in. It;s still happening. If a huge grind. It sounds like the clutch isn;t disingaging and i'm jamming the shifter in while it's still turningand under pressure. ...