Yes, I also have this issue. If I recieve say 3 text messages from one person and then read that particular thread, it will only mark the most recent one as read. I have to click the other messages individually to "read" them. It's quite frustrating!
HTC One in Silver
ROM: Android Revolution HD 7.0
Also have: SPV (Canary), SPV C500 (Typhoon), SPV C550 (Hurricane), SPV M2000 (BlueAngel), SPV M5000 (Universal), TyTNII (Kaiser), Treo Pro (Panther), Touch Pro2 (Rhodium), Desire S (Saga), Desire HD (Ace), One X