Views showing duplicate nodes when filter by domain

Just upgraded to 6.x-2.0, and result was odd behavior in our Views filters.

Let's say you are on host "a.example.com". You have a Views filter which returns all nodes with the "a.example.com" Domain-ID filter. This is a pretty simple filter (we use it for our front page).

Now, let's also say you have nodes marked with both the "publish to all affiliates" flag, and has "a.example.com" as the publish-to affiliate. For nodes with this marking (which happened to be many of the nodes on our site) the views filter is showing these nodes twice.

If I manually edit these nodes and remove the "publish to all affiliates" flag, the duplicate nodes problem goes away. Prior to 6.x-2.0 I was not seeing this behavior.