Thunderbird marks ALL downloaded messages as read on a server, even if I didn't open any of them. E.g. my android mail client doesn't have such problem - message marked as read on a server only when I actually open this particular message.
So if Thunderbird is running in background on my desktop, it keeps marking all incoming mail messages as read automatically. It's annoying, sometimes I miss important messages when checking mail from android, because everything is marked as read.