Chrome should certainly treat requests with varying query strings as different requests; a cached result for style.css?v=123 should never be used for style.css?v=124. If you’re seeing different behavior, please file a bug at http://new.crbug.com/ and post the bug ID here.
That said, I’d first check to see whether the page was cached longer than you expected. If a new version of the page itself wasn’t downloaded, then it would still be requesting ?v=123 as the HTML wouldn’t have changed. If you’re sending long-lived cache headers with the page, it’s certainly possible that Chrome is caching it more aggressively than you expected. If that’s the behavior you’re seeing, please star http://crbug.com/8742 for updates.