**** UPDATE: 4th July 2013, Issue Resovled? ****
I now see this in my metadata XML file!
<?xml version="1.0" encoding="UTF-8"?>
<ApexClass xmlns="http://soap.sforce.com/2006/04/metadata">
<apiVersion>28.0</apiVersion>
<packageVersions>
<majorNumber>1</majorNumber>
<minorNumber>0</minorNumber>
<namespace>packagea</namespace>
</packageVersions>
<packageVersions>
<majorNumber>1</majorNumber>
<minorNumber>0</minorNumber>
<namespace>packageb</namespace>
</packageVersions>
<status>Active</status>
</ApexClass>
Salesforce have listed the issue and fixed here.
One oddity still is that the Versions tab still shows this...

I'll feed this back on my case see if they can explain this.
Original Issue Observations
Yes there is definitely something wrong here.
I have two test managed packages installed and I created the following...
public with sharing class TestPackageMeta {
private packageb__Sales_Invoice__c sinv;
private packagea__WorkOrders__c wo;
}
This resulted in this, no references to the packages...
<?xml version="1.0" encoding="UTF-8"?>
<ApexClass xmlns="http://soap.sforce.com/2006/04/metadata">
<apiVersion>28.0</apiVersion>
<status>Active</status>
</ApexClass>
However the strange thing is this, one reference to package a, but not package b....

Yet reassuringly Show Dependencies showed this...

I also checked that the package dependencies have not been affected and thankfully not...

I've also raised a case on our Premier support contract to see if we can get some traction on this, case number 09403195.