I generally don't rely on progress meters, as they aren't an exact science, as I don't see how they know exactly what has to be scanned ahead of what it is done.
No avast doesn't have anything to do with Microsoft reporting that your Windows isn't genuine, that is the fault of the WGA.
Given the benefit of innocence the WGA has made mistakes in the past on genuine versions, so if that is the case here, you would need to contact your Microsoft number, to have them correct the problem.
Check your system date day/month/year and correct as required.
If it is correct, try a repair of avast. Add Remove programs, select 'avast! Anti-Virus,' click the Change/Remove button and scroll down to Repair, click next and follow. This has in the past resolved this out of sync issue between reported and actual VPS version.