Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
Potential solution

I had the same issue with my icloud "manage storage" panel. The other problem I noticed is that my "sent" messages in the icloud.com webmail application were not showing up either, so I suspect this was a related problem. Until then, I had never bothered to setup my icloud email (me.com) through Outlook as a IMAP on my laptop. When I did that, for some reason, it cleared everything out of my apparent mail storage and the stats reset to "0kb". Not sure what was going on, but that worked for me. Hope this helps!
 
I tried IMAP'ing via Windows Live Mail and also installed the iCloud desktop client but the storage panel still shows 22.4 MB in Mail :(
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.