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[bobmarl33]

Shouldn't the plug-in append the theme stylesheet to the stack last?
it is common practice to use this as a place to override some settings
of plug-in specific settings, but these can be lost if it the sheet is
applied out of order.

[Thaya]

The plugin grabs the stylesheets and puts it in the stack in the order that it finds the sheets. If the theme's stylesheet is displayed in the wrong order (before some plugin stylesheets) then WP Minify will keep things in that order.

I'm looking into giving better control of these stylesheets and javascript in the future. Stay tuned!