Hm.. I've never seen it do that to me (on Windows with multi GB mail storage).
Though I think there is a setting to auto compress the mail storage every so often if it will save more than X, though I can't remember the details on top of my head. If that setting is too low (e.g. if it will save more than 1mb) then it might be running very often for minimal gain.
Perhaps rummage around in there and see if it helps.