Only the emails that I have opened in em client show up as being read when using it. If I open them using my phone or tablet they show as being opened in each other and they used to using Microsoft mail. If I open them in em client they don’t show up when I open them using the other devices. It also just took all of my emails older than one week and made them unavailable to the other devices.
I have tried to reproduce your issue and message stayed unread until refresh.
Does the refresh help or they stay unread until you actually open them in eM Client?
If you still having this issue, please let me know what version of eM Client do you use and how is your account configured.