I believe the post is about HTML <head> section of the document. There are a number of CGI::FormBuilder methods to manipulate how javascript is handled, but I'm not sure there is anything about outputting javascript that won't conflict with other javascript that has previously been generated. For example, what happens if you have two forms and they both output functions with the same name? I have no idea.
Probably the easiest thing is to just disable javascript output for one of those forms. Submission should get checked again anyway on the server side. From the docs on the CGI::FormBuilder constructor:
javascript => 0 | 1
If set to 1, JavaScript is generated in addition to HTML, the default setting.
You can also look at the template section and write your own template (then at least you can control where the javascript goes, if anywhere).
