Mine also sometimes stops at %99 (sometimes can even be %97) , but I've seen %100. But now here comes the real interesting part ; If the battery level falls below the %70-%65s it immediately shows zero, and goes to sleep (the charge is depleted). I plug the cable and it starts charging form %0, it goes about %20s and then immediately jumps to %90s and charges fully at %99-%100. But this generally is because of the misshown percentage. I click to show the time remaing when it is fully charged and it says 7 hours remaining but it actually goes about 2 hours. I launced X resourse Graph and looked at the current level, which now shows 8200mAH (it also shows zero remaining when remaing curent falls below 6500mAH), considering that I've seen values about 3000-3500mAH top when in normal circuimstances.
The repairs and system updates doesn't made any difference. But I didn't try callibration, if I remember correctly it is only under OS9, isn't it?
Don't worry about it, so long as it charges above around 95% indicated full charge. If it won't charge above 95% (after calibration), you might have a bad battery. Apple replaced mine under warranty for this reason.