Well since im having this very same issue, let me add my $0.02...
I have been noticing for almost a month now that my D1 does the same thing. I flash roms regularly as well as kernels. I can fully charge my phone and after I unplug it and use it (texting, few emails, a little music) my battery begins to drop. This is normal. But to me, what is UNnormal is the fact that it will get to 80% and then drop to 50%, then to 20% and the next thing I know, my phone is telling me i'm below 15%.
I do use SetCPU and I only overclock my phone at 700 on ANY kernel. I have tried all kinds of different kernels using the On Demand governor from Chevy's ULV's to P3 Droid's to Sapphire to Slayher's and I still get the same results. This issue just kind of bothers me because I can't fully enjoy these awesome roms like I want to for charging my effin battery every 3-4 hrs. That's ridiculous to me.
Have I tried wiping battery stats? Yes I have. I have tried wiping while the phone was on 100% still plugged in as well as while the phone was on like 5% as well as letting it fully charge and then letting the phone power itself down, fully recharging and repeating, and still I receive the SAME results. Now I'm frustrated.
For those of you who aren't familiar with wiping battery stats, this can ONLY be done in Clockwork recovery mode. SPRecovery will not allow you to do this. How do you get clockwork? The way that I did it was I installed ROM Manager from the market and inside this wonderful app, it will allow you to flash an alternate recovery. I flashed back to 2.0.2.4. This recovery I know will allow me to wipe battery stats and Dalvik Cache. So after doing so, I still.... get the same results. So I have no clue.
If there is anyone who knows what the issue may be, please help us all. I have personally been trying some of everyone's methods and still the same result.