It's possible that there is a glitch in the system or you just need to clear your browser cache. If you're still experiencing this issue and can't find the new certificate you bought so you can set it up, I would suggest calling phone support or doing a live chat. There may be some tweaking they need to do on the back end to help you out.
I am a GoDaddy End User - Just Like You * Please note that I DO NOT answer private messages. Please ask your question in the proper forum so the answer can assist EVERYONE in the community and not just you. If you contact me via PM for help, I will give you a price quote for my personal services. Thanks! *
Once your issue is resolved, please be sure to come back and click accept for the solution