is this the issue you're having?
I'm still searching this forum & others, think my Moto R2D2 (Droid 2) is behaving similarly. I'll post about an "unrelated problem" in the other threads, but ever since OTA Android 2.3.3 in September 2011...
If i choose a contact and begin an SMS conversation, seems like 50% chance their replies will show in a separate thread from mine, such that their contact label in the threads list appears twice: one holds thread of my outgoing txts, other holds all their incoming txts.
This is intermittent. Sometimes (okay, I'll go ahead and say most times, which may negate the 50% as exaggeration!) The SMS thread is generated normally, with alternating mine/theirs txt according to timestamp chronological order.
When i reply to an incoming new txt for which there is no existing thread in my SMS history, i am less likely to end up with this split thread issue. Being spoiled by the normal SMS threading feature, really not enjoying separated txts when trying to follow multiple conversations, especially since some clients have me troubleshoot their computer issues overs SMS after hours. I know, boo-hoo...
Nonetheless, the issue didn't happen until after OTA upgrade from VZW for 2.3.3, of course. I should also mention R2D2 is rooted so i could defeat the bootanimation audio & attempt wireless tether (or not). The issues I'm describing (hopefully in line with OP's description) are all with the stock SMS app, which at least changed in its appearance/theme after the OTA upgrade.
Within 30 days of OTA upgrade my SMS issues began. I used SMS Backup & Restore app to preserve my conversations, then hard reset the phone (after performing other crucial backups), and the issue seemed to disappear. 30 days later with issues reappearing, I took the approach of defeating some keyboard/language features to resolve the problem (see below)...
Meanwhile my other GingeR2D2 issue's include Multi-touch keyboard (on-screen) with word/spelling suggestion features enabled causes SMS and web browser to force close or freeze, even if i use the physical slider) keyboard to type. I bypassed the issue with this workaround: downloaded free app "Gingerbread Keyboard" and switched primary input to that, would use Swype but don't like the layout and am unfamilar with it (will get cozy with Swype some other time, I promise). Another issue, unplanned reboot when using Moto's car dock cradle...
I will post more if I find a resolution. Sidenote: SMS Backup & Restore has a known issue with Motorola's timestamp tagging where restoration of message threads gets wonky on sent vs received times, so possibly my first attempt to restore any conversation after hard reset caused further problems with the SMS app (maybe??). Avoiding the memory reset solution if at all possible!
