There several possible scenarios:
- For some reason W3 is not properly configured or configuration was improperly applied to .htaccess files.
- W3 is properly configured but has compatibility issues with some part of your setup.
- This has nothing to do with W3 at all and comes from some other part of your setup or server.
From this little details it is hard to make educated guess. Aside from generic unnstall/reinstall W3 I can only suggest to try contacting W3 developer with oyur configuration details and your hosting support to check server logs for any visible issues.
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