• I'm sorry to say that this issue still exists in SQL Server 2008 (10.0.4000.0) SP2

    We had it the other day on one of our system test databases that had through a similar scenario to you, with a PK field originally non-clustered, and an IX_BaseTable added as clustered separately.

    Microsoft SQL Server 2008 (SP2) - 10.0.4000.0 (X64)

    Sep 16 2010 19:43:16 Copyright (c) 1988-2008 Microsoft Corporation Enterprise Edition (64-bit) on Windows NT 6.0 <X64>

    (Build 6002: Service Pack 2)