Well neither v1.09 nor 1.09a require CSS/JS Loader as versions v1.06 - v1.08 of TPP did. v1.09 is based on the last release by the original TPP author (before the CSS/JS Loaders was bullied into TPP). Not sure why the CSS/JS Loader would interfere with TPP.. The CSS/JS Loader has no active maintainer here nor is it an add-on available in the Zen Cart downloads (another of many reasons why I felt it needed to unlinked from TPP). You might check with the folks at Numinix or Rubix Integrations for assistance with configuring the CSS/JS Loader..
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