Are you parked on an incline? Does this happen on level ground too? If parked on an incline, and if your e-brake is not fully 'pulled/engaged' the car will move slightly until it rests on the transmission.
btw, this is my first post/reply
I just purchased an 03 6MT coupe last week and have been lurking on this forum since I found it. What a great group!!! and wealth of knowledge!!

 

I usually leave my car in neutral when I park at home.. the only time I keep it in 1st gear is if I'm on an incline or decline.. however the reason why I don't leave it in 1st gear EVERY time is because SOMETIMES I forget that I have the car in gear when I get in and once I start my engine and let go of the clutch I stall and almost hit the car in front of me (very dangerous) so if you leave it in 1st gear everytime just make sure you check your shifter before you start your engine hehehe.

 

Nope, it's pefectly flat. Atleast flat enough not to roll. I was always told to leave the car in 1st just incase the parking break fails. Not sure if that's something that would ever happen, but better safe then sorry.

 

So I guess you were correct before...
maybe a little too impatient with the clutch??

 

If you shut the CAR off first this won't happen

 

ding ding ding right answer. His engine is probably taking longer to shutdown since is has just started it up and it is on high idle.

I always just stop my car leave it in first gear shut the car off and pull the e brake on. Never had a problem.