Your question does not indicate whether you have any documentation that tends to reflect that you complained in writing to the employer about the clock-in system or whether the company acknowledged the problem. If anything of that nature exists, you should present it to EDD at you appeal. Take extra copies of each document. One for you, one for the judge and one for the employer.
Be sure to file your appeal within 20 days of he date indicated on the Notice of Determination that you received from EDD.
You might benefit from consulting with an experienced employment law attorney and having them evaluate your case. The California Employment Lawyers Association maintains a list of employment law attorneys who represent employees against employers. Follow the link to: www.cela.org.