Whoa! steady on there big boy!
It takes 2 or 3 cycles at least before the battery sorts itself out.
See here:-
xda-developers - View Single Post - [KERNEL][2.6.35.14] SiyahKernel v1.8 - Just another android kernel...
"Q: do I need to recalibrate the battery after?
A: battery will be calibrated automatically. if you need to calibrate the battery again, just remove /data/.siyah/battery-calibrated file and reboot. charge at least 6 hours to make sure your battery is full during the calibration."
Q: How does the automatic battery calibration work?
A: Each time you install a new wipe rom, /data partition will be reformatted and you will need to do the calibration again as you lose the calibration data. Automatic battery calibration will wait until your battery is full and delete the battery calibration file to restart the calibration cycle. a new file in /data/.siyah/battery-calibrated will be created. if you want to redo the calibration just delete that file. it is automatic which means you just forget about the calibration. your phone will not be calibrated if it is off. use it normally, leave it connected to charger for several hours and it will be calibrated.
Are you using a governor in SetCPU?
You may need to adjust it to, say, Conservative.