I have the same problem, just got this response from HTC:
Regarding your messages being displayed as oldest to newest instead of the newest to oldest. HTC are aware of this problem thats been caused in there update, and will be releasing a fix for this issue soon. I have informed the escalation team, but as of yet nobody can do anything (software related) to fix this issue. All i can suggest is to either wait until the update/fix arrives for your phone, or if it is a major problem, we can book your phone in for a repair which will fix this issue, but rollback your phone software to 2.1 Aside from this, the update was to improve overall performance of the device, support HTML5 and Flash on the internet, and to imporve the stabililty of sending/receiving texts.
I've installed "Handcent SMS" which seems pretty good