W3TC minify theme's scripts.js causes top menu to dissappear

Hi!  I've just about got all my css and js combined, minified and making Google PageSpeed insights happy using a combination of W3TC and Speed Booster Pack.  However, we are having trouble with the minify on this one last file: 

wp-content/themes/betheme/js/scripts.js?ver=13.3

Everything we try, this seems to make the top menu disappear from the site completely!

Any ideas on best-practices to accomplish this?

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