Hi James,
Those settings are set to true by default in the Web.config shipped with mojoPortal. Often people override a few of them in user.config temporarily while designing based on our Skinning Overview article, however one doesn't even need to disable them for designing any more, there is a way to do it with a cookie so it only affects the designer's browser also discussed in the article.
I tested this morning with the latest code on my local machine with a site configured in a virtual directory and it resolves those urls correctly when CombineCss is false. However, I have a vague recollection of fixing that not long ago so it may be that I fixed it after the release of mojoPortal 2.3.6.7. Getting close to anew release now so that will be fixed in the new release.
Best,
Joe