Im not sure if the issue you are seeing is the same problem that i had. I just built a sql 2008/win 2008 cluster but the problem also existed in sql 2005. it primarily affects ssis. there is a file MsDtsSrvr.ini.xml located here D:\Program Files\Microsoft SQL Server\90\DTS\Binn or where ever yours may be.
If you installed a named instance this is especially problematic. In that file you will see a area with a "." in it which is referring to the default instance. you could change the "." to your sql virtual server name\instance name instead and give it a name like instance's msdb or similar.
look at this page for reference. http://dougbert.com/blogs/dougbert/archive/2009/04/09/ssis-and-clustering-what-you-should-do-instead.aspx .
I have 3 instances so far and the above info works perfectly now.
If this is not your problem then perhaps it will help someone else in the future.