It seems that changes we made back in:
/vesta/vestasys.org/vesta/eval/112
/vesta/vestasys.org/vesta/eval/109.linkdir_ship
Broke the ability to use a relative path as the argument to -shipto. Essentially the cleaning/shipping code that traverses directories assumes that the argument to -shipto is an absolute path.
This should be pretty easy to fix, but has been broken for at least the last three official pre-releases.