According to an e-mail sent off by a member of the Steampowered Forums, an update should be coming shortly that fixes the lack of Milestone unlocks in the latest Team Fortress 2 update. Here is what Valve's Robin Walker had to say about the issue.
So to those of us who are still patiently waiting for the unlocks to roll around, the fix is on the way.
We hope to have the fix out today. Milestone items will continue to not be correctly given to you until we fix it. Once it's out & fixed, we'll run a process to give out all the milestone items that should have been previously dropped.
So to those of us who are still patiently waiting for the unlocks to roll around, the fix is on the way.