I hope this post will save some Domino/Sametime administrator time searching for solution.
I had Domino 5 server with Sametime 3.0 installed on my test server. The server was not in autostart mode. I didn't use it much so I decided to upgrade it to Domino 6.5 for making local tests of STWidget application in Anonymous mode. I chose not to update to the latest Sametime 7.0/7.5 because many (50%?) companies still use Domino 6 and Sametime 3.1/6.5.1. Although Sametime 7 Java Toolkit should work fine with Sametime 6, you never know.
I installed the Domino 6.5.5 server to a new folder and tested that it started correctly. Then I tried to install Sametime 6.5.1 server. The installation aborted with following message:
IBM Lotus Sametime 6.5.1 requires that
IBM Lotus Domino 6.0.3 or later
be installed on the same
computer as IBM Lotus Sametime 6.5.1
Install Domino 6.0.3 or later and
then restart this installation.
I checked that PATH environment variable does not point to the old Domino5 installation and even manually registered the nlsxbe.dll file "regsvr32 c:\lotus6\nlsxbe.dll" and un-registered the dll file in R5 folder.
That didn't help. Then I renamed the folder containing the old Domino 5 server files to c:\aaaaaaaLotus5\, hoping that installation will continue after it failed to open non-existant files.
Now when the new Sametime server installation started, it showed "Path not found" error message. This clearly pointed ou that it was just as I suspected that the old R5 server still was somehow found from the new server installation.
With "Path not found" search string I found IBM's technote describing the solution. The solution was simple: delete the HKEY_LOCAL_MACHINE\SOFTWARE\Lotus\Domino\5.0 registry entry.
After deleting the entry, the new Sametime server was installed without problems.