ok...

I see what you mean now.

I do think it may be something with .png's as well...

"I" myself have never run into this because,... while I use .png's exclusively!!..

I do NOT make them full size images like you are doing.... which is basically like a stack of papers on top of one another..

(lots of layers.. and lots of trans/alpha data to deal with)..

which "I" now believe is leading to your problems.

my suggestion (which may be too much work at this point)..

is make each building an image like it is now.. not ONLY as big as it has to be.. not a FULL IMAGE the size matchign you stage so things align correctly..

but put the X&Y coords in an XML file..and position like..

I can help you whip it up real quick if you like..

(you'll have to do the image work though) =)