Comment 3 for bug 553912

> In other words, the width of the stroke is ignored
> when calculating the offset between clones.

Workaround: temporarily switch to 'Geometric bounding box' mode [1], select the line and create the tiled clones - the stroke width is now included in the width or height of the base tile and takes effect in the calculation of the horizontal or vertical offset (in %) of the 'Shift' parameters. I don't know if this contradictory use of the bounding box mode is intended or just an error when parsing the current bbox mode used for the calculation of the base tile dimensions.
(tested with Inkscape 0.47, 0.48 and 0.48+devel r9828)

[1] Inkscape preferences > Tools > Bounding box to use