I didn't encounter that, but it is worth considering that it might be a coincidence. I've had my share of micro USB connectors wear out to the point where if they're not perfectly positioned, they won't charge, and so I've woken up to a phone that only had a partial charge like yours before if I remember right.
One way to prove it is to backup your current rom, restore your last backup, see if the problem goes away, and restore this one again, and see if the problem returns.
Also consider that you need to run a battery calibration when you install a new rom. that involves charging it to 100% successfully, and then deleting the batterystats.bin file--easiest way is to do that is use this guy's app:
http://forum.xda-developers.com/showthread.php?t=1024867.