To exclude specific sections or JavaScript from optimization (remove Whitespaces, merge JavaScript,...) use the following method (this could be the case for e.g. banners placed by JavaScript):
<!--[borlabs-exclude-start]--> Your section or code which you want to exclude <!--[borlabs-exclude-end]-->
There is no option in Borlabs Cache to exclude JavaScript code of a specific plugin. If something isn't working after you have activate to merge JavaScript, the chance is 99% that one JavaScript has a syntax error and the correct way to fix that is to fix the code and not exclude the code from the merging process. If you need help to find the JavaScript file with the broken syntax, just ask our support.