I am cross-posting this from bug 0006749, because the same save file and process demonstrates bug 0006590:
I can reproduce the bug as originally described. I have created a save file for convenience, though I don't think it is specific to any save file.
Debian Wheezy 7.5
Linux 3.2.0-4-amd64 <POUND>1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
1) Fresh unpack of Dwarf Fortress 0.40.02 SDL from http://www.bay12games.com/dwarves/df_40_02_linux.tar.bz2 [^] [^]
2) Fresh unpack of bug6749.zip from http://dffd.wimbli.com/file.php?id=8894 [^] [^]
3) Press ESC 3 times (to get past intro), then choose "Continue Playing."
4) Load region "bug6749"
5) Center on the miner.
6) Unpause, then watch as the root is dug out (already designated, though not visibly indicated), then the entire tree vanishes, and the roots turn into Silty Clay Loam Wall!
Also, same results with Windows 7 Pro SP1 32bit, updates current.