I'm not sure at all, but do you have a rule set up that all Read emails are sent to the Deleted folder? Unread emails wait to be read, but as soon as you open them, read them then pass on to the next, do they automatically move to the Deleted Items folder?
If so, check your web-based GMail account again. If they are being marked as read there, perhaps they are arriving in OE and going straight to the Deleted Items folder for that reason.
I am trying to set up Gmail to go through my Outlook express. I am using Outlook Express Six and windows XP SP3 if it matters. I found some very good instructions on how to do this on the Internet. Setting it up went very well, when I press "Send and Receive" it shows that it is receiving the message, but it is downloaded into my "Deleted Items" folder. I went into the message rules and made sure I had nothing in there that would send the mail to my deleted folder. I really have no idea what to do next. People on this forum have been VERY helpful in the past and I am hoping you will be able to help me with this.