One solution would be to give your custom Button style a name and then give your buttons that styleName. Perhaps not an optimum solution because you will have to do so with every button (though cascading from your primary containers would also work.)
Another solution is to set the skins for the buttons via the maximizeButtonSkin, minimizeButtonSkin, and restoreButtonSkin styles. Perhaps even just setting them to their respective defaults would work:
/**
* Skin for maximize button when using Flex chrome.
*
* @default mx.skins.halo.WindowMaximizeButtonSkin
*/
[Style(name="maximizeButtonSkin", type="Class", inherit="no",states="up, over, down, disabled")]
/**
* Skin for minimize button when using Flex chrome.
*
* @default mx.skins.halo.WindowMinimizeButtonSkin
*/
[Style(name="minimizeButtonSkin", type="Class", inherit="no",states="up, over, down, disabled")]
/**
* Skin for restore button when using Flex chrome.
* This style is ignored for Mac OS X.
*
* @default mx.skins.halo.WindowRestoreButtonSkin
*/
[Style(name="restoreButtonSkin", type="Class", inherit="no",states="up, over, down, disabled")]