SPSite.Usage.Storage is wrong and I can't find the “large” files

A user's MySite is over the default quota of 100MB.

PS C:\> $site.Usage.Storage106731646

So the user currently has round about 106MB in his personal site. The problem is: He doesn't.

Database:

SELECT 
SUM(Size)
  FROM [SP_Content_MySites].[dbo].[AllDocs]
  WHERE DirName LIKE '%personal/username%'
  AND SIZE IS NOT NULL
  AND SIZE !=0-->3993036

So he actually has 3,9MB in his personal site.

I checked his recycle bin (that's where the 3,9MB comes from) as well as the second stage recycle bin (empty). I don't know where the 100MB comes from and I don't know how to "update" the quota - by that I don't mean to increase it. Is there some cleanup timer job I need to run? Any more Powershell voodoo I can try?