If one is clearing and one is not, then the add-on functionally is working, e.g. no known or obvious bugs. There is something very specific going on for the site that is not clearing, and since you’re using file it leads me to believe that it has to be a permission error and it’s unable to delete the cache file. The next step is to debug the CacheBreaker.php->_breakEntryCache() function to see if anything is going wrong in that function. If you can var_dump, step debug, or log that function it might reveal something. Have you checked your php error logs? B/c it will try to log an error if it exists. At the bottom of that function is this:

try {
            if (count($clear_tags)) {
                $this->clearTags($clear_tags);
            }

            if (count($clear_items)) {
                $this->clearItems($clear_items);
            }

            if (count($refresh_items)) {
                $this->refreshItems($refresh_items);
            }
        } catch (\Exception $exception) {
            error_log($exception->getMessage());
        }