Diskeeper has to comply with both laws, but it's up to the plaintiffs under which statute they wish to bring their suit. They could've even claimed that Diskeeper violated both FEHA and EEOC claims (or merely EEOC claims); but claiming violations under the EEOC would've permitted Diskeeper an opportunity to remove the case to Federal Court. There is no argument for removal to Federal Court where the only bring state claims.
The EEOC is not relevant here, as the Complaint cites California state causes of action only (which keeps the case in state court as opposed to federal court). California's FEHA statute is similar to the EEOC, with the exception that FEHA permits unlimited compensatory and punitive damages, whereas EEOC damages are capped.