\newcommand{\Matrix}[1]{\boldsymbol{#1}} $\Dot{\Matrix{A}}$ $\dot{\Matrix{A}}$
The dot is offset to the left of the apex of the A because the A is italicized.
I guess that the problem lies with the \boldsymbol, because everything looks OK if the A has normal weighting.
no, only a problem of the italic mode ...
$\skew{7}{\Dot}{\Matrix{A}}$
Herbert