MySQL Grouping Error
Perhaps you could look for the number of records for each usageUser as well
This query will give the record count for all users per division
SELECT count(1) usageUser_Records,L.divisionName,R.usageUser 
FROM records R 
INNER JOIN locate L  
    ON L.computerID=R.usageComputerID
WHERE R.usageWhen LIKE &quot;2012-07-08T12:%&quot;
GROUP BY L.divisionName,R.usageUser;

This query will give the record count for all divisions per user (reversed GROUP BY)
SELECT count(1) usageUser_Records,L.divisionName,R.usageUser 
FROM records R 
INNER JOIN locate L  
    ON L.computerID=R.usageComputerID
WHERE R.usageWhen LIKE &quot;2012-07-08T12:%&quot;
GROUP BY R.usageUser,L.divisionName;

Looking back at your original query, if removing the count(distinct usageUser) gave you the same number of rows, my guess would be that 2012-07-08 has either one division or one user being retrieved. Looking back at your original post, you said you inherited this data. Chances are, there is only one division or one user throughout the data.
This may not be a full answer but just two suggested queries to get you to think. I hope this helps...
UPDATE 2013-08-06 12:48 EST
As suggested by @yercube
SELECT count(1) usageUser_Records,L.divisionName,R.usageUser 
FROM records R 
INNER JOIN locate L  
    ON L.computerID=R.usageComputerID
WHERE (R.usageWhen &gt;= '2012-07-08T12:00:00' AND R.usageWhen &lt; '2012-07-08T13:00:00')
GROUP BY L.divisionName,R.usageUser;

This query will give the record count for all divisions per user (reversed GROUP BY)
SELECT count(1) usageUser_Records,L.divisionName,R.usageUser 
FROM records R 
INNER JOIN locate L  
    ON L.computerID=R.usageComputerID
WHERE (R.usageWhen &gt;= '2012-07-08T12:00:00' AND R.usageWhen &lt; '2012-07-08T13:00:00')
GROUP BY R.usageUser,L.divisionName;