After some gracious time with SAP's Jonathan Brown we found that there are server config files and database entries that remain after the 4.1 uninstall that retain that the product version is 4.1...
One example is BusinessObjects_WebIntelligence_dfo that is read on CMS server startup
Located in
D:\Program Files (x86)\SAP BusinessObjects\SAP BusinessObjects Enterprise XI 4.0\dfo\
So, there seems to be some issues in the uninstall of the 4.1 server and we are exploring are options- including trying to get windows server restored, but have lately found out we cannot restore back to the dates needed.
Or, a new server install and migrate content using promotion manager....argh.
Or, wait for the patch that caused us to have to bail out of 4.1 in the first place. It might be included in BI 4.1 SP2 1.7 in March... http://scn.sap.com/message/14659164
I think I learned something in all this, because it hurts, so it must be good for me.
Lee Lewis