fyi, I was able to implement a setting you can use to fix the background color issue which only happens in IE and only in some skins. The setting disables the extra clear type corrections in the cycle plugin and this is what creates a background for the slides so disabling it solves this. However the side effect of disabling it is that in IE slides with text will have a slight grainy look to the font for a brief second until the main clear type corrections are applied.
This new setting will be in the next release.
Best,
Joe