You may want to check the details of your source PNG, and your version of GD. PNG files can either be truecolor, or have a 256 color palette. GD only started supporting the output of paletteless PNGs as of v2.0.

Even if you have GD 2.0, you probably want to call GD::Image->trueColor(1) before constructing the object, either that or use GD::Image->newFromPng($file,1)