Hi Steve!
Sorry for the late answer, I missed your previous post.
I can see your site, and I cannot see any problem.
I tried some search on your Google Custom Search, and I always get appropriate results. I tried it with Chrome, Firefox and Internet Explorer, and everything was right.
Here are some solution to the problem that you mentioned above:
https://productforums.google.com/forum/#!topic/customsearch/pJl44MeAs4Q;context-place=forum/customsearch
According to the forum posts, try to switch off any solution that you use for load scripts faster, or try to use another search engine.
We are going to do some improvements in the next version, to use API v2 instead of API v1.
Peter