I so that eMclient have the same issue tha thunderbird - dont chect for new messages in subdir in inbox.
My server automaticly move new messages to subdir - for example form *@comany-a.pl all messages was moved to dir inbox\company-a, from *@company-b.com to inbox\company-b etc. All mesages they wasn’t marked as readed.
eM client was check this dir only when I manually enter on it (then detect it as new).
Aquamail on my andorid device was work as perfect with it.
My version is 7.2.33277.0 but on 7.1 is the same problem.