Aleem Bawany's Google Custom Search works well with WordPress. I was using it for some time. Then I changed something and added new CSE code in the CSE Search Box. and then it stopped working. Why? Because I have added different CSE code and that was not ready for iframe. I was looking for how to fix it. I have forgotten how I set it first time.
Go to Look and feel of Google CSE under Control Panel and select Iframe under Choose a Hosting Option.
Then go to Get Code section and Specify search results details. It is
http://www.satya-weblog.com/search/ for me. Replace with your host name. Now your Search box code is ready. Copy and paste it on Search Box code place.