I thought this was resolved in one of the 1.4.6 snapshots, but then it seems to be back in the full version of 1.4.6.
I've been having this happen in the prerelease for 1.4.6 lately. I've noticed this has happened with pickaxes; not sure about other tools.
Alright; thank you!
This has happened with me when I've been in jungle biomes. Of course, the trees appear when I restart Minecraft. Survival, single-player. I seem to have had a problem related to this with cacti as well.