I think this started with the latest WP-Supercache (0.6.5), but the normal (old style) WP-Cache part doesn't seem to work anymore on my end. I had a friend of mine take a look and he offered the following bug report:
If one uses mod_deflate and the user requesting a page accepts gzip, the stored page in ./cache is the gzipped version without a corresponding 'content-encoding: gzip' header in ./meta. Supercached pages are unaffected.
PHP version: 5.1.6
Apache: Apache/2.2.3 (CentOS)
Hope this helps.