Could you zip the save from the start of SoA and the CHR file of your character at the end of BG1:EE?? Upload it using the attach a file option at the bottom of the comment box. CHRs are in Documents/Baldur's Gate Enhanced Edition/characters, save a in Documents/Baldur's Gate Enhanced Edition/save.
I can confirm what thespace said, it has nothing to do with importing. The problem is caused simply by pressing the dual-class button. I have figured out how the stealth score is reduced: The points taken away are the character's current base stealth points according to the ranger's stealth ability table (SKILLRNG.2da). So pressing the dual-class button without actually dual-classing somehow strips away the ranger's base stealth score. The stealth points from other sources stay in place, i.e. stealth points from dexterity, from race, and the bonus points of the Stalker and Beastmaster.
@hook71: Thanks. Can you also make sure this is reported for both Enhanced Editions (in case you haven't already)? Because as @thespace indicated, this also happens in BG:EE, not just BGII:EE.
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CHRs are in Documents/Baldur's Gate Enhanced Edition/characters, save a in Documents/Baldur's Gate Enhanced Edition/save.