I don’t currently use W3TC, but I have looked at it a while ago. If you have cleared the cache, the next area I would suggest looking at is the minification & concatenation module.
I will set it up on one of my test sites to try to reproduce your issue & investigate how to fix it . Please provide a link to an affected page on your site, so can see exactly what the issue is.
i had to remove w3 from the site in question because it was a live site and the tabs were in a significant part of the organization that i couldn’t afford to have broken.
so i tried to reproduce the issue on other sites that i have with the same theme, but wasn’t able to reproduce the issue. strange. maybe, as you mentioned, it’s the w3 settings for this one particular page, although i usually set them up the same with all of my sites… perhaps another plugin conflicting with w3 as well.
You could test this by deactivating all other plugins and then activating them one by one, however testing plugin conflicts with a cache plugin still active is not much fun.
