I can confirm that with Ubuntu 12.04, Dia 0.97.2-5 the bug is no longer present.
In fact the window layout is considerably different with this version of Dia,
the tool kit and layers box are no longer free floating separate items, but
rather all part of one single window.
This bug can be marked as closed.
** Changed in: dia (Ubuntu)
Status: Confirmed => Fix Released
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https://bugs.launchpad.net/bugs/892815
Title:
[Oneiric] Layers support is completely broken in Dia
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