I think I fixed the filter area clipping on squeezed objects. I committed it to the trunk; please test and report if it works for you, then I will commit it to the 0.45 branch also.
Note that it still does not work entirely correctly for squeezed and rotated objects, but this cannot be fixed quickly because, once again, we differ with Batik on a more fundamental level: Batik makes the filtarea itself rotated, whereas in Inkscape it always remains horizontal/vertical. I guess we should hide this difference by just always making the filterarea large enough so that its edges are not seen in Inkscape _nor_ in Batik, but I can't so far find a formula which would give such "large enough" - but not too large - margins. Anyone who's better at math than me can give it a try in new_filter_gaussian_blur().