Either of these worked fine in 6.5.2-8:
convert \( -size 200x200 xc:black \) \
\( -size 100x100 xc:white \) \
-gravity center -compose over -composite \
-alpha copy \
-background red -alpha background \
tmp_alpha2_red.png
or
convert \( -size 200x200 xc:black \) \
\( -size 100x100 xc:white \) \
-gravity center -compose over -composite \
+clone -compose copy_opacity -composite \
-background red -alpha background \
tmp_alpha2_red.png

but produces this in IM 6.5.2-9:
