Since Avogadro 0.9.8 it is no longer possible to add new atoms in a new file when the user doesn't have administrator priviledges. This occurs on Windows XP 32 bit and also 64 bit version. This is a regression to Avogadro 0.9.6 (maybe also to 0.9.7).
We haven't heard any other reports of this, is it still happening for you?
Marking as pending...
Yes, this bug does not occur in Avogadro 1.0.