If an Attack Power is say Dex vs. AC, but you're using a Heavy Throw weapon (which is then based on Strength) does the Power still count from Dex?
No, the attack power should be used as written.
Heavy Thrown - Compendium (emphasis is mine):
A thrown weapon is a ranged weapon that is hurled from the hand, rather than used to launch a projectile. A ranged basic attack with a heavy thrown weapon uses the wielder’s Strength modifier for the attack and damage rolls, unless otherwise noted in the description of the power used.
In the Players Handbook, page 216/17, weapon properties are described. I assume you have already read through this but, the description of 'Heavy Thrown' weapons is
'You hurl a weapon thrown from you hand, rather than using it to loose a projectile. A ranged basic attack with a heavy thrown weapon uses your Strength instead of your Dexterity for the attack and damage rolls.'
This would indicate that the Str instead of Dex rule applies only to heavy thrown weapons when they are used in basic attacks and not powers. However, as a player I would speak to my DM about this. If the power is something that heavily relies upon accuracy, perhaps Dex should be the determining attribute, regardless of weapon used. If, however, it is simply a ranged weapon power, I would ask my DM to use Str as the determining attribute when using heavy thrown weapons.
As a DM I would let my players use Str but, if you want to solidly stick to the rules, only basic attacks. Hope this helped.