Ghost4u - Yes, some mail servers will mark messages as read on the server when they're accessed over POP3. This is actually very common.
Now of course you'll see the change in webmail (which basically *is* your mail server), and then in AquaMail if it connects using IMAP (which has message state sync, unlike POP3).
The messages are staying unread in Outlook because I'm guessing you're using POP3 there, which does not support message state sync, so each message's unread state is tracked by Outook on its own in its local message storage.
slfolkes - Since you mention Yahoo, which should have been configured by the app using IMAP, I'm thinking this must be a different issue. I could investigate if you recorded a debug log capturing this happening:
http://www.aqua-mail.com/?page_id=232