I am using the Android stock Email app. When I read the email on Gmail (via web login), Android Email is not being updated to show "read". Yahoo mail works fine.
Check the settings on the stock app to see if it's IMAP or POP3. If you can't tell, delete the account from that email app, then add it back and let it set up as IMAP. (If the account itself is POP3, change it - POP3 is for using only 1 email program on an account.)