Hi John,
Regarding the first problem you are right it is a bug it should not disable the javascript loading from scriptloader if you disable it on the stylesheetcombiner.
This is now fixed in the repository if you pull changes then run update.
Regarding the menu issues, this is most likely caused by the change to .NET 4 and corresponding differences in menu behavior. I .NET 4 they use some javascript to set some styles on the menu. I encountered problems with menus on a number of the included skins when we first changed to .NET 4.
You could solve it easily by changing this setting in Web.config <pages ...controlRenderingCompatibilityVersion="4.0" to 3.5
but I would recommend not doing that since you lose some benefits of .NET 4 doing that and it is possible to solve the problems with CSS.
What I found by using Firebug was that hard coded styles are applied to the menu by javascript and some of these may contradict what you have in CSS. The only way to fix it is to add !important on the styles in your css that are being changed by javascript.
Example from andreasviklund-02:
div.AspNet-Menu-Horizontal { margin: 0px 0px -9px 0px !important; padding: 10px 0px 0px 0px; width:100%; height: 29px; background: #e0e0e0; float:none !important; }
I had to add the !important in those places to fix it. You may need different things, the trick is to inspect with firebug and figure out what is contradicting your css.
Best,
Joe