When I run it on a WSS 3 install that has SQL 2005 Express installed on the same server, it gives me this error eight times:
"Error connecting to SQL Server
An error has occurred while establishing a connection to the server. When connecting to SQL Server 2005, this failure may be caused by the fact that under the default settings SQL Server does not allow remote connections. (provider: SQL Network Interfaces, error: 26 - Error Locating Server/Instance Specified)"
I'm running it with this string:
sharepointbpa.exe -cmd analyze -substitutions SERVER_NAME SharePoint3
I don't have more details. On my box the tool worke fine.
For such problems please post into the public newsgroup or open a support case with Microsoft.
I have found a work around for this try it,