Doesn't sound like an issue, esp because you say it's working correctly. It may be a relevant piece of info if the amp had some other issue but a 2-3-C° difference between channels shouldn't be a concern.
Is there adequate ventilation around it, is it in a rack with other gear, and/or are any air inlet/outlet passages blocked?
I couldn't say without more info.
Is this the same amp that you changed the fan (or fans) on? Maybe a different fan speed or different CFM spec could affect temperatures across the channels.
If you're still concerned, I'd recommend a quick call to HARMAN Pro Tech Support.