I installed 2009 and now I am having issues with 2008. The toolbar icons look like 2009 icons and when I close the program I get the message "CUI file 'acad.cui' is an incompatible format and can not be overwritten".
I've found that to avoid any incompatibility problems I remove 2008 (and remove all the scratch files left on the PC drive) before ever installing 2009. If you have to have both then there are certain folders that you have to keep the customization files separate. That seems to go for CUIs, plotting control files (that aggravating linked shortcut for both plotting wizards; sure wish they'd add the version number to the name so they could live in the same company standard directory), tool palettes, to mention a few.
I've never seen this clearly documented but it is a real problem. If you inter-mix the CUIs you can also get the ribbon section corrupt also. I think some of this comes through the Workspaces also.