I can confirm this with 0.44 on my Ubuntu Karmic (64-bit) system. The only way to get indented checkboxes there is to use codemonkeys workaround.
Indenting works well though on my netbook which is also running 0.44 on Ubuntu Karmic (32-bit). I can't think of any relevant difference in the personal settings of both systems.
I can confirm this with 0.44 on my Ubuntu Karmic (64-bit) system. The only way to get indented checkboxes there is to use codemonkeys workaround.
Indenting works well though on my netbook which is also running 0.44 on Ubuntu Karmic (32-bit). I can't think of any relevant difference in the personal settings of both systems.