I’m out here at PASS this week and was in the CAT area. Cindy Gross (who works for MS and blogs here) hooked me up with someone who let me know that what I found back in May (where if you changed your path for install, things like log shipping wouldn’t work after failover) has been fixed. This is GREAT news. 

The fix can be found in SQL Server 2008 SP1 CU10 and it didn’t get finished in time for SP2, but it will be in SQL Server 2008 SP2 CU1.  

So how do you deal with the problem if you’ve already deployed?
Well, installing the CU won’t fix the issue. You’d have to slipstream the CU into your 2008 install, remove the node, and re-add the node to SQL Server. I am not saying evict the node in Failover CLuster Manager – just run the normal remove process for SQL Server.

How do you ensure that all new deployments do not have this issue?
Slipstream the CU before running Setup.