I'm seeing the same issue, though it is different than you describe.

In my case, where I don't have tips, the SS wages are completely blank!  So, you may have this case as well, only your tips wages are also being included, and they normally reduce the SS wages box.

I duplicated this as well, but then got both the latest payroll updates and installed the latest QuickBooks patch release, R7, and then it worked.

There was no warning to install updates and no form error that the numbers were wrong, only that I'd overpaid taxes (which I had not) because it omitted the SS wages and tax using the prior QB release.

Intuit's in for a wild ride on this one.  Sheesh.