After upgrading to Lotus Notes Traveler 8.5.0.1 Interim Fix LO39586, mails disappear from the device inbox when read in Notes client.Prior to this fix, mails stayed on the device and changed read / unread marks according to the Notes Client.
Downgrading to 8.5.0.1-LNT-LO37251 fixes this issue.
http://www.eknori.de/2009-04-24/lnt-mails-disappear-from-inbox/