Are you using the mail app for the exchange accoutn in Exchange Mode or POP3/SMTP or IMAP mode?
How long between syncs (settings, accounts & sync, chose the account for your exchange, Account Settings, Amount to Sync and Email Check Frequency)?
I use mine in Exchange mode, I sync 2 weeks worth and I sync it every 15 minutes. If I read an email on my Droid and then immediately check it on my outloock client then I get the same as you. If I wait 15 minutes they will both read the same as far as Read or Unread. YOu could set it to PUSH but your battery life will suffer. It's all about give and take.
hmmm...good question. The only way I know is during installation of a new account, you chose exchange mode. I've never set up a pop3 or IMAP so I don't know what the settings look like. Actually, I take that back. On day one when I took my droid home I chose POP3 and niticed it wasn't working right so I deleted it an hour later. But my CRS won't let me recall that far back. LOL
Try setting up a new account and chose Exchange mode and see if the two accounts look the same. You can always delete the extra one later. Do you know your exchange settings or do you have a corporate IT person who sets the phone up for you?