what are your fill settings (stroke/fill etc)
I use OS X SL and have not seen this problem - could you post the whole svg file.
hopefully some one with more experience will come along with the answer but I'll try to help if I can!
I can't seem to use the fill tool in Inkscape (v0.48 on OS X). Trying to fill a rectangle object with a 0.010 mm line width (stroke color: blue) with no fill while sectioning off a chunk with a two-node straight line cutting through the upper half. I tried filling the area, but it only filled it and left a weird uneven margin on the end (http://www.flickr.com/photos/25968780@N03/5552182877/). Clicking the white margin doesn't do anything. I also tried changing the line width to something thicker, making it the same color as the straight line, but same seems to have no effect. Checked for gaps, found none. I also tried changing the threshold, but that just made it not fill anything at all. What am I doing wrong?