Comment 1 for bug 902054

> Some (maybe 2 or 3) layers should be visible by default.

They are usually, if you use a Gtk+ theme with "normal" scroll bar widgets. In my tests, the minimal initial height of the list of layers is determined by the minimal size of the Gtk+ widget (arrows + minimal length of scroll bar slider).
Are you possibly using Inkscape on Ubuntu with the custom scroll bar overlay? (please add information about OS/platform and Inkscape version when filing reports).

Based on my earlier tests, this could be the same issue as
Bug #884368 in Inkscape: “unable to edit attributes in XML Editor”
<https://bugs.launchpad.net/inkscape/+bug/884368>