@heddle – There shouldn’t be any discrepancy in the image count due to which nav you are using. The way the plugin works, all the image are pulled into the panels and the nav is built after the fact. The 3.0.1 update was showing the right number of posts for the default nav when I released it… this is what I way primarily testing. If there is a discrepancy, it should be obvious because the number of panels in the code will exceed the count on the slider. If this is the case, I would like to take a look at it.
You can mess around with the code all you like while keeping your changes upgrade-proof. If you read the documentation, you can use the hooks and filters to change how the slider works. The navigation numbers are generated with jQuery, so that might be hard for you to change if you don’t work with jQuery.
The background image for the navigation and title can easily be changed by dropping a few lines into your theme’s css file:
div.promo_slider_title{background:none;}
div.promo_slider_nav{background:none;}
This will clear out the background images (version 3.1.0 allows you to check a box on the options page in the admin to do this), but you will probably want to add your own styling after that.
If you have a specific style in mind, send me a mock up and I will see if there are some simple things I can do to make the plugin more flexible.