I had this problem too. What I did was open my BG:EE save game in EEKeeper (http://forum.baldursgate.com/discussion/16497/ee-keeper-updated-to-v1-0-2/p1), clicked the "custom portrait" button, selected the portrait I wanted to use in BG2:EE, and clicked export (once for each size). This saves the .bmp to "My Documents/Baldur's Gate - Enhanced Edition/portraits", just copy this folder over to "My Documents/Baldur's Gate II - Enhanced Edition/portraits" and use the "customize" button on the "records" screen to pick your new portrait.
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