As a sidenote, I wanted to congratulate you on your site design. It really kickz @zz! I still didn't get any errors when I went to your site, but i'm using Opera and it's not the best at reporting errors.
Now, onto your question. Typically javascript and CGI shouldn't have any problems coexisting with each other. I use javascript rollover menus on my site, and it works fine. Here are some suggestions for narrowing your problem down:
First, try inserting only the header into the control panel. If you get the error then, you know it's in the header. If not, try with just the footer (leaving the header blank). Do that until you find out which one is really causing the error.
Once you figure that out, try replying to this post, and include your exact header or footer (whichever is causing the problem) in a CODE tag maybe, so we can analyze exactly what code seems to be causing the conflicts. Then we might be able to tell you what's up.
---Skorpion