Mine's been getting quite toasty as of late, but I think it has something to do with the northeastern heatwave. Since temps started crawling into the high 80s/low 90s, I've been getting the amber/green flash indicator (
thread here), the battery gets quite a bit warmer than normal and it ceases to charge properly. I've had my Eris since December, and this has only been happening for the last week or two, which is consistent with the rising temperatures in my area (as well as my lack of AC).
If the amber/green flash is happening, I've noticed that's when the charging issues arise. It happens about 15-20 minutes after I plug in the charger on any surface in my house, and after a cool down time equal to (and optionally including) the time it takes to reboot the Eris, I've managed to duplicate that result several times.
My solution has been to take the back cover off of it and lean it up against the back of a box fan on high while it's charging. Instead of blinks in 15 minutes, it's been solid amber for well over an hour and charging normally. I haven't experienced any inability to unlock the phone from the security screen or boot-up issues like some of you are mentioning, but it's not to say I necessarily won't soon.
For right now, if you want a quick fix, either charge it in the path of your AC output, or take the fan route. I'm content with doing that and not having to send my Eris back to HTC, I love it.