This is a well-known issue, and is mentioned in
/usr/share/doc/chkrootkit/README.FALSE-POSITIVES and in the upstream
FAQ: http://www.chkrootkit.org/faq/#8

Simply put, chkrootkit should not contain a whitelist of acceptable
dotfiles by default, as a rootkit could simply use the files listed in
the whitelist as known good hiding places.

That being said, the newer Debian/Ubuntu packages contain a patch that
adds a "-e" option that lets administrators add their own whitelist. I
think this is a reasonable idea and it should be included in the hardy
package so chkrootkit can be used by system admins without constantly
getting false positives.

-- 
chkrootkit falsely flags files owned by Firefox 3 and Sun Java 6 valid packages
https://bugs.launchpad.net/bugs/575945
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