When installing MOSS in an 2008R2 environment, you will notice that the Best Practices Analyser for Sharepoint will not run.. now this is not only to the fact that the BPA is running on the 2008R2 environment, it’s when the entire sharepoint farm is running on 2008R2. One  option is to have a single 2008/2003 server on the same farm and point to that, or wait for the next release of BPA for Sharepoint.

The error received would be: Failed to retrieve the configuration database connection string from machine ‘<insert machinename>’ due to the following error: Failed to retrieve the configuration database connection string from machine ‘<insert machinename>’

The problem with Sharepoint on 2008R2 and most tools (MossRap tool also) is that they query the 32 bits Registry, and that option is not available anymore in 2008R2 (while it was on 2008 even x64). More info:

http://msdn.microsoft.com/en-us/library/aa384129(VS.85).aspx

Either KEY_WOW64_32KEY or KEY_WOW64_64KEY can be specified. If both flags are specified, the function fails with ERROR_INVALID_PARAMETER.

And in the tool (as for the moss rap scoping tool) we see the query:
int regAvailable = RegOpenKeyEx(hRemoteKey, @”SOFTWAREMICROSOFTSHARED TOOLSWEB SERVER EXTENSIONs12.0SECURECONFIGDB”, 0, KEY_QUERY_VALUE | KEY_WOW64_64KEY | KEY_WOW64_32KEY, out hTargetKey);//return 0=registry available

Microsoft is looking into the problem and has already created a new version of the MOSS rap scoping tool a new BPA will probably be released shortly