Quoth MediaWiki.org info page for the VipsScaler extension: "The VipsScaler extension is a wrapper around VIPS, a free image processing software. VIPS is a set of image manipulation tools specially designed for speed and low memory usage. This is useful for resizing large PNGs, and it improves the appearance of shrunken JPEGs."
Sounds like it could be a possibility.
Here's some info. I've only uploaded one file to test so far, but it's http://en.brickimedia.org/wiki/File:ToaMeiko_Avatar.png
As you can see in this screenshot, the non-thumbnailed full-size photo up top is correct, but in the version history where it's thumbnailed it still shows the old revision.