I'm not sure if this is the same thing you are talking about, but I had something similar happen before:
I downshifted a few times with one clutch squeeze and got it into neutral, still holding the clutch in at the stop. When it was time to go I went to press it into 1st and it wouldn't. Then a friend told me to let go of the clutch and pull it back in and try. Like butter.
Not sure why this happens but it has happened a few times if I don't let the clutch out and re-squeeze.
My suggestion would be when you downshift from third to second, let the clutch out in second, then re-apply clutch for the second to neutral transition, and the same thing for neutral to first. Hope this helps...
:cheers