SQL Server 2005 Patch Corrupts SQL Installation on Windows 2003 Standard x64

We're in a holding pattern on this one right now, but I thought I'd poll folks for some added info in case this has happened to anyone else.

We have 2 SQL 2005 Enterprise servers on Win2K3 Std x64. We installed the MS08-040 patch last year and it ended up corrupting the master database on both servers. It looked from the logs like it was mistakenly replacing 64-bit server binaries with 32-bit binaries. MS PS said it was due to 32-bit client tools being installed on the server and told us to take the 32-bit tools out.

I completely removed the client tools from the servers and reran the patch with the same results. I've had to put them back because we need to use them in our apps.

Everything worked fine on our 32-bit installations and even on our 64-bit development server. Since I'm anticipating getting marching orders at some point to install SP3 (which includes this patch) I'm grasping at anything right now to see if we can get some more info on this. We've also implemented the workaround for MS09-004 (which replaces MS08-040) instead of installing it.

Has this happened to anyone else? If so, were you able to work through it?

Yes, I have experienced this also on a deployment machine. After the patch of SP3 the SSIS stuff is completely broken amongst a few other things.

We are planning to re-install the entire server and migrate the databases over to a server that is PRE-installed with SP3.

We don't know what happened but I would expect that lots of people have had a similar issue.