Then something else local to your device is causing this issue. The stock mail app is super simplistic. This is the same app across other HTC devices.
Assuming you are not rooted and you don't have another mail app installed that can interfere, it's going to be a setting that you are overlooking.
I have 9 email accounts on the stock mail app and they are all separate, unless I want to view all at once.
I am using imap.