Well, after the machine goes into standby the CPU is still warm, and still needs to be cooled, so I wouldn't automatically assume this is a problem.
I just did a check of my machine to see of when it went to standbye the fans would still cool the CPU and tythe others would keep running...
All my fans went off when the machine went to standbye!!
What I would like to know is do you have any fans that are hooked to some sort of Fan speed controller and NOT hooked to the mobo?
I wish you luck in getting to the bottom of this perplexing problem!!