Does aggregating JS/CSS interfere with my drupal_add_js()?
Yes, drupal will definitely miss your custom JS scripts in it's js aggregation build phase, if you're loading JS on different pages. This is because by the time a user (or you) hits the other pages, the aggregated js file has already run previously, and created the cached JS file it thinks is all it needs. It uses this cache file until the cache is cleared or the crontab is run.

A couple of options are to either:


try using the drupal_add_html_head() function to add the js when ever you want, or,
write some js to detect what library is needed (perhaps based on a data attribute element in the markup), and then conditionally load the other js via the getScript method.


Good luck.