I have both versions now
Originally got my EVO about 30 days after launch and it is version 003. Friend of mine also has 003 two months after launch.
I had an issue that ended up not being the EVO but Sprint sent me a refurbished 002.
I have fully inspected both units and cannot find ANY differences, including the battery door.
My 003 has a very slight light leak along the bottom of the screen which I did not notice before because my case was on. No other issues that others are reporting.
I have been using the 002 refurb for a week now and the only thing I can say for sure is that it is getting noticeably better battery life than my 003 did, which I always thought was good anyway.
In fact, my only complaint I do have is that the 002 refurb has some scratches and a creaky kickstand, but that's not EVO's fault.
I suspect some folks bought some early hardware revisions that may gotten out by mistake. I base this on reports of very obvious hardware differences that most are not seeing.
The Sprint support rep said 003 had some issues and very few were released, however he could not say exactly what the issues were. Sounded like rumor to me. Another rep said he had not heard of any 003 issues at all.