Hi Erhan,
It is a matter of personal taste, myself I think titles on the top are more natural and on the bottom is unexpected, though in the gallery either choice seems ok.
The reason for the change though was mainly because we changed to also use the colorbox for other things like the help files and the skin preview dialog and in these cases having the title on top seems even more important whereas in the gallery it seems ok either on top or bottom.
In any case you can override it from CSS. If you look in style.config you can figure out which colobox theme you are using and you can override it in your custom css files as long as you custom file is lower in the list of included files in style.config.
Adding something like this might do it, but you may need to study the colorbox CSS and do some experimentation to get what you want:
#cboxTitle{position:absolute; bottom:-22px; left:0;}
Hope that helps,
Joe