Was experiencing similar behaviour in Synaptic on Jaunty.
Checked what would happen when using apt-get:

WARNING: The following packages cannot be authenticated!
---snip---
Authentication warning overridden.

So in my case it wasn't a Synaptic bug. Checked /etc/apt/apt.conf and
found "APT::Get::AllowUnauthenticated 1;". Changed it to "0" and the
warning dissappeared for both apt-get and Synaptic.

So not so much that "packages cannot be authenticated" as "packages will
not be authenticated". Perhaps the wording of the messages could be
improved?

-- 
Packages not authenticated
https://bugs.launchpad.net/bugs/33696
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