At work, we have a policy of setting the compiled *.class files with the same timestamp as the .java files they come from, to ease up auditing of what classes actually change. It's not difficult to touch them so they'll have the same timestamp down to the second... but then, the milliseconds difference remains (where the .class has ".000" and thus is "older" than its corresponding source with its, say, ".666" value), which screws the report up.
So far, I've dealt with this by touching my .java files with their own timestamp, forcing them all to be ".000", but it's annoying and stinks of a kluge (and if I ever forget to do so before doing a delivery...).