Which version of SS are you running. I remember it was an issue but works fine 2.4

Only thing I can think of is your environment includes and older version of the GD library that doesn't support imagesavealpha(). The function used to keep transparency (its called in the silverstripe GD wrapper). I know I've had this problem on certain hosts when their "default" php build is missing some updated or usually included modules. Takes forever to debug those

Hmm should be working, I know its working on 2.4.2 which leads me to believe its something to do with your specific install. Try writing a specific function to resize a png and see if fails. Something like this
http://www.akemapa.com/2008/07/10/php-gd-resize-transparent-image-png-gif/

Also check your logs to see if there's any error. I know the GD library actually needs a lot of memory if you're resizing a lot large images.

Finally check to make sure there aren't any extra alpha channels or paths in your image I know that has cause weird errors in the past for me