This is a known issue. There has been reports in the past (I've also seen it happen myself at a couple of sites). There's no pattern to it. Sometimes, some mail disappears, sometimes only a particular user's mail disappears, and all of a sudden it works perfectly again.
I believe I read in devinfo that that's one of the reasons Mitel moved away from using obtuse to mailfront begining with SME 5.5.
Kelvin