I may be missing the boat here and simply telling you what you already know but 3 people in my office all experienced the same issue when installed Mercury QC and noone knew what was going on..... Our WINLOGON.INI file was wiped out in the C:\WINDOWS directory.
Well it turns out when you turn off UAC (Windows Vista User Access Control) it takes you to a different place giving you the "opportunity" to create a new SAPLOGON.INI file!!! If you turn UAC back on your old INI file magically reappears. If you want UAC off, because it's a major PAIN and some programs don't work well with it on (Mercury Quality Center is one), then make a copy, turn UAC off and then copy the INI file to the C:\WINDOWS directory and you are good to go.
Can't wait until they sunset Vista !!!