I'm trying to create depth effects with the "interpolate" extension and I'm getting weird results.

In the following example, I would like to create a kind of cone from the interpolation of two discs A and B (top part of the image link. However, in some cases, the interpolate extension shifts the position of the end shape B (which makes the results unusable for my purpose, cf attached image, lower part). Have you already heard about this problem ?
It 's a bit strange because sometimes the result is just fine. It seems that the problem may occur when shapes A and B intersect each other but it's still unclear for me.

Any idea?

http://imageshack.us/photo/my-images/268/interpolate.png/

This is a known issue, and there are very good explanations of what to do about it elsewhere in this forum, especially ~suv's posts on the subject.
But just some quick hint(s):
1.you may have moved the smaller circle before doing the interpolate.
2.You also may have "preserve transforms" instead of "optimized" checked in your inkscape preferences.
3.Or you may have resized your document at some point.
4.The objects may be in a group that has been transformed.
5.The objects may be ellipses, which may somehow retain their transform attribute even if you have "optimized" selected in prefs, so you need to convert object to path, and move it a little to lose the transform.

To see if the object has a transform, select it and open the xml (ctrl-shift-x) ...

Upload a svg if this doesn't help and someone will take a look in there...

druban wrote:But just some quick hint(s):
(…)
5.The objects may be ellipses, which may somehow retain their transform attribute even if you have "optimized" selected in prefs, so you need to convert object to path, and move it a little to lose the transform.

6. Alternatively, update to the latest stable release (0.48.2) - the bug has been fixed in the meantime:

• Bug #518768 in Inkscape: “Interpolate disregards rotation/skew state of an ellipse”
  (and its variations in the duplicate reports)