Before the December update (or sometime around recently), I had to play with minifcation order in manual mode. It'd seem like I would get it, but something with Firefox and W3TC was unreliable and it would seem like there was a caching problem with changes not being reflected (I completely disabled the browser's caching with a plugin).
The best I could figure out was that the webfont CSS files had to be at the top of the minification, and one had to be over the other.
My two webfonts were a custom font from Icomoon and a font I created with FontSquirrel's engine. Are you using either of those?
But until some bigger issues are resolved (like why 0.9.2.8 is actually slowing down my site), I have disabled the plugin.