You don't provide a lot of detail so its not clear, but it is possible the problem you are seeing is identical to or similar to this...
Font references in CSS such as Bootstrap are usually relative like this:
src:url(../fonts/glyphicons-halflings-regular.eot)
The simplest way to require no changes when using such CSS in Salesforce (and get the fonts to work) is to have one static resource ZIP containing both the CSS and the fonts with this internal folder structure:
bootstrap
bootstrap.min.css
bootstrap.min.js
fonts
glyphicons-halflings-regular.eot
glyphicons-halflings-regular.svg
glyphicons-halflings-regular.ttf
glyphicons-halflings-regular.woff
The CSS can then be referenced in your page using e.g.:
<link href="{!URLFor($Resource.BootstrapZip, 'bootstrap/bootstrap.min.css')}"
rel="stylesheet" />
which is delivered to the browser as e.g.:
<link href="/resource/1416590327000/BootstrapZip/bootstrap/bootstrap.min.css"
rel="stylesheet" />
so that the relative reference to the font resolves to the valid URL of:
/resource/1416590327000/BootstrapZip/fonts/glyphicons-halflings-regular.eot
If the CSS and fonts are in separate static resources, then at best you will have to modify the CSS to use the font static resource name, and at worst you might even end up including the resource version timestamp.