Seems to be working now, I used:
SELECT TOP 100 PERCENT
dbo.tblComputers.Computername AS Computer,
dbo.tblComputers.Username,
dbo.tblComputers.Lastseen
FROM
dbo.tblComputers
WHERE
computername NOT IN (SELECT DISTINCT dbo.tblComputers.Computername FROM dbo.tblfileversions INNER JOIN dbo.tblComputers ON (dbo.tblfileversions.Computername = dbo.tblComputers.Computername) WHERE dbo.tblFileVersions.FilePathfull LIKE '%SmcGui.exe%')
ORDER BY
dbo.tblComputers.Computername
The INNER JOIN seemed to be my problem.
Something that may help a bit is a way to filter out the PC's that are having errors (about 8% of our PC's can't be scanned for one reason or another, not a LS problem). If anyone has the code it would help, otherwise no big deal, I'll work it out when I have more time.