Specific Query runs fine directly or when any change to it is made but in current state takes longer to run

Major Update after a couple days of debugging:

I run a few queries similar to :

SELECT RTRIM(part) as part 
FROM tableP pm 
LEFT join tableS s on pm.id = s.id 
INNER JOIN tableC cm ON cm.id = pm.id 
WHERE name = 'NGW'  AND  status NOT IN ('NL', 'Z') 
GROUP BY RTRIM(part), isnull(s.value,0) 
ORDER BY isnull(s.value,0) 

It is run in Java li开发者_如何学Cke so:

    PreparedStatement select = con.prepareStatement(
        "SELECT RTRIM(part) as part" +
        "FROM tableP pm " +
        "LEFT JOIN tableS s ON pm.id= s.id " +
        "INNER JOIN tableC cm ON cm.id= pm.id " +
        "WHERE name =? AND  status NOT IN ('NL', 'Z') " + 
        "GROUP BY RTRIM(part), isnull(s.value,0) " +
        "ORDER BY isnull(s.value,0) " );
    select.setString(1, name);
    ResultSet rs = select.executeQuery();
    while(rs.next()){
          ... Data is Loaded...

The queries have been running fine inside of a Java application. Suddenly 3 or 4 queries of this form went from taking less then a second to over a minute.

I have copied the exact query from SQL Profiler and when run directly on the database it preforms in less then a second. I started to make changes to the query and found any change to the query would return it to 1 second performance even adding a single space between a statement. But as soon as I returned it to its original exact state it would take 60+ seconds.

Core Question: So, I have a fix, but what could cause a query to run differently even with just a change as small as whitespace?

Is it possible that the execution plan is corrupted? Can you try explicitly clearing the plan cache? http://msdn.microsoft.com/en-us/library/aa175244(v=sql.80).aspx