Hi,
Probably used by you Custom CSS has mistake in syntax that damaged whole rest. Probably you forgot to add "}" or different small mistake. This is one of the main reasons. If nobody touched template core files.
Always check your Custom CSS using CSS Validator (Online or from Software). We all make mistakes and that tool help us find them.
To fix it, Select & Cut whole custom CSS from Custom CSS Area, Save settings and paste to Notepad, and check again Template Options. Then if all will be OK, check your CSS syntax (!).
Using custom.css file is better - read Helix Guide for details.