This post pretty much sums up everything that was learnt by theGanymedes (and others) in the entire thread.
Here's my advise:
1. Don't use a sense rom as the power drain is too high and you'll find the phone will cut out before it starts charging (even after you've plugged in the cable). Use Cyanogenmod (or Oxygen) and this app. You can work around this but it's a pain in the neck.
2. Read carefully the section entitled Make the calibration permanent (thx to user "theGanymedes") as this is the bit that will solve the problem.
3. I did read somewhere that once you have set the new Full40 value it is a good idea to discharge and recharge the battery again but in reality you only need to drop to 80% and then charge back up. This may not matter at all but I thought I'd mention it.
4. When you do finally discharge the battery to empty (or charge whilst the phone is off) your battery's age (Batt Age %) will increase to 94% again (the default) but you can safely ignore this so-long-as you've set your Full40 value correctly above.
5. Do enable the advanced options in the app's settings else you wont see the option to send values to setreg in the LearnPrep tab. This may be self evident but I've seen a few people caught out by it (including me ).
Hope this helps.