Erebus: As a general rule, if you are having problems deciding between two interpretations of the rules, usually the most restrictive position is the correct one.
In this case, nothing suggests that a strength drained character polymorphed into a troll wouldn't be a strength drained troll. By the arguement that 'damage follows the body', there is no reason that a person polymorphing into another creature wouldn't heal ALL hit points, for who, being wounded, is going to deliberately transform into a wounded being?
Arguements about where the damage is going, ignore the real heart of the issue which is what the game mechanics say. In this case, they are largely silent, so you should assume that the strength drain transfers to the new form in an intuitive fashion and the only additional effects are those which are explicitly described in the rules.
Generally, ask yourself this question. If I was in trouble, which way would I not want my DM to rule? That is the correct ruling.
If you must come up with a justification, explain that attribute drain is damage to the characters 'life force' - a mystical source of power which does not vary regardless of form.
(Actually, as a side note, that could be justification for house ruling that Con did not vary with form either, which would help to restore balance to polymorph spells.)