Hi Samantha,
The problem is known to the developers, it is casued by the lazy load of IE and nothing to do with any of the themes in Moodle.
If you open IE and view your site, then click on F12 (function key) you will the screen you are viewing will split horizontally and in the lower half of the screen you will see the HTML source for the page. You should also see a tab marked "CSS" click on it.
Now the HTML changes to a list of CSS selectors and properties.
Just below the CSS tab you will see an 'arrow' another icon with a red X through it,(this is the clear cache icon), next to that the nornal 'save file' icon and next to this a drop-down menu which has if you open this you will see a selection of style.php urls amongst which is a set of YUI-combo.php files. If you click on the last of these the CSS canges to the YUI CSS used for the menu.
If you look closely down this CSS list you will see one of the properties of background-image: as a sprite.png
Go down this list and un-check the 'tick-box' at the side of this all those YUI CSS selectors whose property is this sprite.png image. Eventually you will get to the one which is causing the white overlay effect in the menu. When you find this make a note of the YUI CSS selector and add this to the CSS stylesheet for your custom splash theme.
You will need to add this to make sure it disables it...
.yui3-skin-sam .yui3-menu-horizontal .yui3-menu-label {
background-image: none!important;
}
You will find also that the following CSS is used for all the hover instances where the blue might appear, so as a test add this and where ever you see "red" as a background you will know the CSS you have running will over-ride the YUI CSS, just change the RED to a color of your choice.
div.yui3-menu.custom_menu_submenu .yui3-menu-content li a:hover,
.yui3-skin-sam .yui3-menu-label-active,
.yui3-skin-sam .yui3-menu-label-menuvisible,
.yui3-skin-sam .yui3-menu .yui3-menu .yui3-menu-label-active,
.yui3-skin-sam .yui3-menu .yui3-menu .yui3-menu-label-menuvisible,
.yui3-skin-sam .yui3-menuitem-active .yui3-menuitem-content,
.yui3-skin-sam .yui3-menu .yui3-menu .yui3-menuitem-active .yui3-menuitem-content,
.yui3-menu-content li:hover { background-color: red; }
Some times I use red, yellow, green and blue and other colours to test where each one goes... so if you split them up and add them as seperate items you will see which colour is used in the menu.
div.yui3-menu.custom_menu_submenu .yui3-menu-content li a:hover{ background-color: red; }
.yui3-skin-sam .yui3-menu-label-active{ background-color: yellow; }
.yui3-skin-sam .yui3-menu-label-menuvisible{ background-color: green; }
.yui3-skin-sam .yui3-menu .yui3-menu .yui3-menu-label-active{ background-color: blue; }
.yui3-skin-sam .yui3-menu .yui3-menu .yui3-menu-label-menuvisible{ background-color: orange; }
.yui3-skin-sam .yui3-menuitem-active .yui3-menuitem-content { background-color: purple; }
.yui3-skin-sam .yui3-menu .yui3-menu .yui3-menuitem-active .yui3-menuitem-content { background-color: white; }
.yui3-menu-content li:hover { background-color: gray; }
By adding all the above group of CSS items you will be able to (hopefully) make sure the menu works like YOU want it to.
I hope this helps?
Mary