Desc: I've seen it happen many times. If you click on a birch tree, and something accidently makes you disengage from it before you take the CNR out, it disappears.
EDIT: I think I also noticed this with Hazelnuts, and ginseng seems to do the same as well.
Location: Silkwood Forest, possibly other Birch places, ginseng, hazelnut
Date: Since August 09
Verified/Reproducable: Many times... Gosh Darnit. Click on one twice from a distance. (I've tested this with cotton and blackberry bushes and this doesn't happen to them)